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2017

  1. P. Skums, A. Zelikovsky, R. Singh, W. Gussler, Z. Dimitrova, S. Knyazev, I.Mandric, S. Ramachandran, D. Campo, D. Jha, L. Bunimovich, E. Costenbader, C. Sexton, S. O'Connor, G. Xia and Y. Khudyakov, "QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data," Bioinformatics, 2017, to appear
  2. Y. Khudyakov, I. Mandoiu, P. Skums, A. Zelikovsky, “CAME 2017: 6th Workshop on Computational Advances in Molecular Epidemiology,” Proc. of ACM BCB 2017, p. 775, publisher url
  3. I. Mandric, Y.T. Tiagueu, T. Shcheglova, S. Al Seesi, A. Zelikovsky and I.I. Mandoiu, "Fast Bootstrapping-Based Estimation of Confidence Intervals of Expression Levels and Differential Expression from RNA-Seq Data," Bioinformatics, 2017, pdf preprintpublisher urlbibtex
  4. E. Gerasimov, A. Zelikovsky, I. Mandoiu, and Y. Ionov. "Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire," BMC Bioinformatics, 18(8):244, 2017.  publisher url
  5.  N. Yu, X. Guo, A. Zelikovsky, and Y. Pan, "GaussianCpG: a gaussian model for detection of CpG island in human genome  sequences," BMC Genomics, 18(4):392, 2017.  publisher url
  6. D. Jha, P. Skums, A. Zelikovsky, Y. Khudyakov, and R. Singh, “Modeling the Spread of HIV and HCV Infections Based on Identification and Characterization of High-Risk Communities Using Social Media,” Proc. of International Symposium on Bioinformatics Research  & Applications (ISBRA), 2017, Lecture Notes in Bioinformatics 10330, pp. 425-430. publisher url,  bibtex
  7. I. Mandric, S. Knyazev, C. Padilla, F. Stewart, I. I. Măndoiu, and A. Zelikovsky, “Metabolic Analysis of Metatranscriptomic Data from Planktonic Communities,” Proc. of International Symposium on Bioinformatics Research  & Applications (ISBRA), 2017, Lecture Notes in Bioinformatics 10330, pp. 396-402.  publisher url,  bibtex
  8. A. Artyomenko, P. B. Icer, P. Skums, S. Ramachandran, Y. Khudyakov, and A. Zelikovsky, “Agent-Based in Silico Evolution of HCV Quasispecies,” Proc. of International Symposium on Bioinformatics Research  & Applications (ISBRA), 2017, Lecture Notes in Bioinformatics 10330, pp. 420-424. publisher url,  bibtex
  9. S. Mangul, H. Yang, F. Hormozdiari, E. Tseng, A. Zelikovsky, E. Eskin, “HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads,” IEEE Transactions on Nanobiosciences 16(2), pp. 108-115, 2017.
  10. R.W. Harrison, Mandoiu, and A. Zelikovsky, “Guest Editors’ Introduction to the Special Section on Bioinformatics Research and Applications,” IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)14(3) pp.  576 - 577 (2017)
  11. P. Skums, and A. Zelikovsky, "Guest Editorial Introduction to the Special Issue on Bioinformatics Research and Applications," IEEE Transactions on NanoBioscience 16(2) (2017): 79-80.
  12. A. Artyomenko, N. C. Wu, S. Mangul, E. Eskin, R. Sun, A. Zelikovsky, "Long single-molecule reads can resolve the complexity of the Influenza virus composed of rare, closely related mutant variants," Journal of Computational Biology, 2017,  publisher url
  13. A. Rogovskyy, D. Gillis, Y. Ionov, E. Gerasimov, and A. Zelikovsky, "Antibody response to Lyme disease spirochetes in the context of VlsE-mediated immune evasion", Infection and Immunity85:e00890-16, 2017

2016

  1. Z. Cai, A. Zelikovsky, "Special issue on Computing and Combinatorics Conference," Theoretical Computer Science 609: 515, 2016, bibtex
  2. Z.Cai, A. Zelikovsky, “Computing and Combinatorics,” Algorithmica, 76(4) (2016) pp. 865-866.
  3. I.I. Mandoiu and A.Z. Zelikovsky (Eds.), Computational Methods for Next Generation Sequencing Data Analysis, John Wiley & Sons, 2016,publisher urlbibtex
  4. P. Skums, A. Artyomenko, O. Glebova, S. Ramachandran, D. S. Campo, Z. Dimitrova, I. I. Mândoiu, A. Zelikovsky, and Y. Khudyakov, “Pooling Strategy for Massive Viral Sequencing,” In I.I. Mandoiu and A.Z. Zelikovsky, editors, Computational Methods for Next Generation Sequencing Data Analysis, Wiley, 2016, pp. 57-84.
  5. S. Mangul, N. C. Wu, E. Nenastyeva, N. Mancuso, A. Zelikovsky, R. Sun, and E. Eskin, “Applications of High-Fidelity Sequencing Protocol to RNA Viruses,” In I.I. Mandoiu and A.Z. Zelikovsky, editors, Computational Methods for Next Generation Sequencing Data Analysis, Wiley, 2016, pp. 85-104.
  6. I. Mandric, J. Lindsay, I. I. Mândoiu, and A. Zelikovsky, “Scaffolding Algorithms,” In I.I. Mandoiu and A.Z. Zelikovsky, editors, Computational Methods for Next Generation Sequencing Data Analysis, Wiley, 2016, pp. 107-132.
  7. O.Glebova, Y. Temate-Tiagueu, A. Caciula, S. Al Seesi A. Artyomenko, S. Mangul, J. Lindsay, I. I. Mândoiu, and A. Zelikovsky, “Transcriptome Quantification and Differential Expression From NGS Data,” In I.I. Mandoiu and A.Z. Zelikovsky, editors, Computational Methods for Next Generation Sequencing Data Analysis, Wiley, 2016, pp. 301-328.
  8. P. Skums, A. Artyomenko, O. Glebova, D. S. Campo, Z. Dimitrova, A. Zelikovsky, and Y. Khudyakov, “Error Correction of NGS Reads from Viral Populations,” In I.I. Mandoiu and A.Z. Zelikovsky, editors, Computational Methods for Next Generation Sequencing Data Analysis, Wiley, 2016, pp. 331-354.
  9. B. Tork, E. Nenastyeva, A. Artyomenko, N. Mancuso, M. I. Khan, R. O’Neill, I. I. Mândoiu, and A. Zelikovsky, “Reconstruction of Infectious Bronchitis Virus Quasispecies from NGS Data,” In I.I. Mandoiu and A.Z. Zelikovsky, editors, Computational Methods for Next Generation Sequencing Data Analysis, Wiley, 2016, pp. 383-400.
  10. ​Y. Temate-Tiagueu and S. Al Seesi and M. Mathew and I. Mandric and A. Rodriguez and K. Bean and Q. Cheng and O. Glebova and I.I. Mandoiu and N.B. Lopanik and A. Zelikovsky, "Inferring metabolic pathway activity levels from RNA-Seq data," BMC Genomics: 17(Suppl 5):542, 2016, pdf preprintbibtex
  11. J. He,  Y. Li, and A. Zelikovsky, "Guest Editorial: Introduction to the Special Issue on Bioinformatics Research and Applications," IEEE Transactions on NanoBioscience 15(2) (2016): 72-74. publisher url,
  12. A.G. Bourgeois, P. Skums, X. Wan, A. Zelikovsky (Eds.)  Bioinformatics Research and Applications - 12th International Symposium, ISBRA 2016, Minsk, Belarus, June 5-8, 2016, Proceedings. Lecture Notes in Computer Science 9683, Springer 2016
  13. S. Mangul, H. Yang, F. Hormozdiari, E. Tseng, A. Zelikovsky, E. Eskin, “HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads,” Proc. of International Symposium on Bioinformatics Research  & Applications (ISBRA), 2016, Lecture Notes in Bioinformatics 9683, pp. 80-92 publisher url,  bibtex
  14. A. Artyomenko, N. C. Wu, S. Mangul, E. Eskin, R. Sun, A. Zelikovsky, "Long single-molecule reads can resolve the complexity of the Influenza virus composed of rare, closely related mutant variants,"  Proc. the 20th Annual Intl Conf on Research in Computational Molecular Biology (RECOMB) 2016, Lecture Notes in Bioinformatics 9649, pp.164-175. publisher url,  bibtex
  15. M. Mathew, K.I. Bean, Y. Temate-Tiagueu, A. Caciula, I.I. Mandoiu, A. Zelikovsky, and N.B. Lopanik, Influence of symbiont-produced bioactive natural products on holobiont fitness in the marine bryozoan, Bugula neritina via protein kinase C (PKC), Marine Biology 163(2): 44, 2016, publisher url,   bibtex

2015

  1. X. Ding, J. Wang, A. Zelikovsky, X. Guo, M. Xie, and Y. Pan, "Searching high-order SNP combinations for complex diseases based on energy distribution difference," IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 12(3): 695-7042015 
  2. I. Mandric and  A. Zelikovsky, "ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching," Bioinformatics,    31(16):2632-2638, 2015, (.pdf) publisher url,  bibtexcitations
  3. I. Mandric and  A. Zelikovsky, "ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching," Proc. the 19th Annual Intl Conf on Research in Computational Molecular Biology (RECOMB) 2015, Lecture Notes in Bioinformatics 9029, pp. 222-223 publisher url,  bibtex
  4. P. Skums, A. Artyomenko, O. Glebova, S. Ramachandran, I.I. Mandoiu,  D. S. Campo, Z. Dimitrova, A. Zelikovsky, and Y. Khudyakov, "Computational Framework for Next-Generation Sequencing of Heterogeneous Viral Populations using Combinatorial Pooling," Bioinformatics, 31(5):682-90, 2015,  Epub 2014 Nov 13 citations  bibtex publisher url
  5. A. Artyomenko, N. C. Wu, S. Mangul, E. Eskin, R. Sun, A. Zelikovsky, “2SNV: Quasispecies reconstruction from PacBio reads,” ICCABS 2015.
  6. E. Nenastyeva, A. Zelikovsky, Y. Ionov, I. I. Mandoiu: Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire,” ICCABS 2015.
  7. P. Skums, O. Glebova, D. S. Campo, N. Li, Z. Dimitrova, S. Sims, L. Bunimovich, A. Zelikovsky, Y. Khudyakov, “Algorithms for prediction of viral transmission using analysis of intra-host viral populations,” ICCABS 2015 .
  8. N. Yu, X. Guo, A. Zelikovsky, Y. Pan, “GaussianCpG: A Gaussian model for detection of human CpG island,” ICCABS 2015.

2014

  1. S. Al Seesi, Y.T. Tiagueu, A. Zelikovsky and I.I. Mandoiu, "Bootstrap-based differential gene expression analysis for RNA-Seq data without replicates," BMC Genomics 15(Suppl 8):S2 , 2014, publisher urlbibtex citations
  2. Z. Cai, A. Zelikovsky, and A. G. Bourgeois (Eds.), Computing and Combinatorics - 20th International Conference, COCOON 2014, Atlanta, GA, USA, August 4-6, 2014. Proceedings. Lecture Notes in Computer Science 8591, Springer 2014.
  3. J. Lindsay, H. Salooti, I.I. Mandoiu and A. Zelikovsky, "ILP-based maximum likelihood genome scaffolding,"  BMC Bioinformatics, 15(Suppl 9):S9, 2014, publisher url, , bibtex  citations
  4. S. Mangul, S. Al Seesi, A. Caciula, D. Brinza, I.I. Mandoiu and A. Zelikovsky, "Transcriptome Assembly and Quantification from Ion Torrent RNA-Seq Data," BMC Genomics 15(Suppl 5):S7, 2014, pdf  preprint,  publisher url,  bibtex citations
  5. S. Mangul, N. C. Wu, N. Mancuso, A. Zelikovsky, R. Sun, E. Eskin, "Accurate viral population assembly from ultra-deep sequencing data." Bioinformatics 30(12): 329-337 (2014) publisher urlurl, bibtex  citations
  6. A. Artyomenko,  N. Wu, S. Mangul, E. Eskin, R. Sun, and A. Zelikovsky, “Reconstruction of Influenza A Virus Variants from  PacBio Reads”, ICCABS 2014, pdfpublisher url bibtex
  7. I. Astrovskaya, N. Mancuso, B. Tork, S. Mangul, A. Artyomenko, P. Skums, L. Ganova-Raeva, I.I. Mandoiu and A. Zelikovsky, “Inferring Viral Quasispecies Spectra from Shotgun and Amplicon Next-Generation Sequencing Reads,” in Genome Analysis: Current Procedures and Applications,  Maria Poptsova ed.,  Caister  Academic  Press,  2014, pp. 231-262. citations
  8. S. Al Seesi, S. Mangul, A. Caciula, A. Zelikovsky and I.I. Mandoiu, “Transcriptome reconstruction and quantification from RNA sequencing data,” in Genome Analysis: Current Procedures and Applications,  Maria Poptsova ed.Caister Academic  Press, 2014, pp 39-60. citations
  9. Leos G. Kral, A. Caciula, Y.T. Tiagueu, and A. Zelikovsky, "Assembly and Annotation of the Etheostoma tallapoosae Genome." Plant and Animal Genome XXII Conference. Plant and Animal Genome, 2014. publishers url, pdf

2013

  1. P. Skums, O. Glebova, A. Zelikovsky, Z. Dimitrova, D.S.C. Rendon, L. Ganova-Raeva, and Y. Khudyakov, “Alignment of DNA Mass-Spectral Profiles Using Network Flows,” Proc. of International Symposium on Bioinformatics Research  & Applications (ISBRA), 2013, Lecture Notes in Bioinformatics 7875, pp. 149-160. publisher urlbibtex  citations
  2. P. Skums, N. Mancuso, A. Artyomenko, B. Tork, I.I. Mandoiu,Y. Khudyakov and A. Zelikovsky, “Reconstruction of Viral Population Structure from Next-Generation Sequencing Data Using  Multicommodity  Flows”,  BMC  Bioinformatics  14(Suppl 9):S2, 2013, publisher url citations
  3. Q. Cheng, P. Berman, R. Harrison, and A. Zelikovsky, “Efficient Alignments of Metabolic Networks with Bounded Treewidth,” in Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics, in Y. Pan, J. Wang, and M. Li, ed.Wiley Book Series on Bioinformatics, 2013, pp. 413-430. 
  4. T. Alsulaiman, S.K. Prasad, and A. Zelikovsky, Distributed Algorithms for TDMA Link Scheduling in Sensor Networks, International Journal of Networks and Computing 3(1), pp. 55-74, 2013,  publisher urlbibtex citations
  5. I. Mandoiu, J. Wang and A. Zelikovsky, “Guest Editors’ Introduction to the Special Section on Bioinformatics Research and Applications,” IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)10(6) pp. 1345-1346 (2013) publisher urlbibtex

2012

  1. J. Lindsay, H. Salooti, 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 pdf preprint,publisher urlbibtex  citations
  2. ​S. Mangul, A. Caciula, S. Al Seesi, D. Brinza, A. Rouf Banda, R. Kanadia, I.I. Mandoiu and A. Zelikovsky, An Integer Programming Approach to Novel Transcript Reconstruction from Paired-End RNA-Seq Reads, Proc. ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2012, pp. 369-376 pdf preprintpublisher urlbibtex  citations
  3.  J. Chen, I. Măndoiu, R. Sunderraman, J. Wang, A. Zelikovsky,  “Guest Editors’ Introduction,”  BMC Bioinformatics 13 (Suppl10): S1 2012,  publisher urlbibtex
  4. 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, publisher url, bibtex  citations
  5. G. Calinescu, C. G. Fernandes, H. Kaul and  A. Zelikovsky. “Maximum Series-Parallel Subgraph," Algorithmica 63, pp. 137-157, (2012) publisher urlbibtex  citations
  6. 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) pp. 1002-1003 (2012) publisher urlbibtex   
  7. 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, publisher urlbibtex  citations

2011

  1. 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. 237-249, 2012,  publisher urlbibtex  citations
  2. 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,publisher urlbibtex citations
  3. 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  publisher urlbibtex citations
  4. 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, pp. 118-123, 2011, pptpublisher urlbibtex  citations
  5. 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, pp. 94-101, 2011, ppt, publisher urlbibtex  citations
  6. 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, LNBI 6833, pp. 213-224, 2011, pdf preprintpublisher urlbibtex citations
  7. I. Astrovskaya, B. Tork, S. Mangul, K. Westbrooks, I.I. Mandoiu, P. Balfe and A. Zelikovsky, “Inferring Viral Quasispecies Spectra from 454 Pyrosequencing Reads,” BMC Bioinformatics ,  12(Suppl 6):S1, 2011,  pdf preprintpublisher urlbibtex  citations
  8. 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 pdf preprintpublisher urlbibtex  citations
  9. J. Chen, J. Wang and A.Z. Zelikovsky, “Preface,” in Proceedings of International Symposium on Bioinformatics Research and Applications (ISBRA 2011), J. Chen, J. Wang and A.Z. Zelikovsky (Eds.), LNBI 6674, 2011 pp. vi-x.  publisher urlbibtex
  10. 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) pp. 865-866 (2011)  publisher urlbibtex
  11. 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), publisher urlbibtex  citations

2010

  1. B. Pasaniuc, R. Garfinkel, I. Mandoiu and A. Zelikovsky, “Optimal Testing of Digital  Microfluidic  Biochips,”  INFORMS Journal of Computing23(4),  pp. 518-529, 2010, pdf preprintpublisher urlbibtex  citations
  2. 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),  LNCS  6506, pp. 16-24, (.pdf)  citations
  3. 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 (ICDM), 2010, pp.687-694 (.pdf). citations
  4. 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 (ICDM), 2010, pp. 679 – 686 (.pdf). citations
  5. 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. (.pdf) citations
  6. 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 (.pdf)  citations

2009

  1. X. Cao, Y. Wang and A. Zelikovsky, "Scheduling Bursts using Interval Graphs in Optical Burst Switching Networks," Proc. IEEE GLOBECOM, December 2009, pp.1-6, (.pdf).  citations
  2. Y. Li, I.I. Mandoiu and A. Zelikovsky, “Editorial,” International Journal of Sensor Networks, 6(1) (2009), pp. 1-2. (.pdf).  (url)
  3. I. Astrovskaya and A. Zelikovsky, “Genotype Tagging with Limited Overfitting,” Proc. of Brazilian Symposium on Bioinformatics, July 2009, LNBI 5676, pp. 1-12. (.pdf).  citations
  4. P. Berman, M. Karpinski and A. Zelikovsky, “1.25-Approximation Algorithm for Steiner Tree Problem with Distances 1 and 2,” Workshop on Algorithms and Data Structures (WADS), August 2009, LNCS 5664, pp. 86-97. (.pdf).  citations
  5. S. Gremalschi, G. Altun, I. Astrovskaya and A. Zelikovsky, “Mean Square Residue Biclustering with Missing Data and Row Inversions,” Proc. of International Symposium on Bioinformatics Research  & Applications (ISBRA 2009),  May 2009, Lecture Notes in Bioinformatics (LNBI)  5542, pp. 28-40, (.pdf). citations
  6. 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. (.pdf).    
  7. Q. Cheng,  R. Harrison and A. Zelikovsky, “MetNetAligner: a web service tool for metabolic network alignments,” Bioinformatics25 (15):1989-1990, 2009.  citations 
  8. Q. Cheng and A. Zelikovsky, “Network Mapping of Metabolic Pathways,” Analysis of Complex Networks: From Biology to Linguistics, M. Dehmer and F. Emmert-Streibto (eds.), WILEY-VCH Verlag GmbH & Co., 2009, pp. 271-293. citations
  9. A. Zelikovsky: “Bottleneck Steiner Tree Problems.” In Encyclopedia of Optimization, 2nd edition, C. A. Floudas and P. M. Pardalos (eds.), Springer 2009, pp. 311-313.  citations

2008

  1. Q. Cheng, P. Berman, R. Harrison and A. Zelikovsky, “Fast Alignments of Metabolic Networks,” Proc. of IEEE International conference on Bioinformatics and Biomedicine (BIBM 20008), pp.147-152, (.pdf)  citations
  2. 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. (.pdf)
  3. I. Mandoiu, R. Sunderraman and A. Zelikovsky, “Preface,” in Proceedings of International Symposium on Bioinformatics Research and Applications (ISBRA 2008), I. Mandoiu and A. Zelikovsky (eds.), Lecture Notes in Bioinformatics, LNBI 4983, Springer 2008, pp. vi-x. (.pdf)
  4. K. Wesbrooks, I. Astrovskaya, D. C. Rendon, Y. Khudyakov, P. Berman and A. Zelikovsky, “HCV Quasispecies Assembly using Network Flows,” Proc. of International Symposium on Bioinformatics Research  & Applications, May 2008,  LNBI 4983, pp. 159-170.  (.pdf)  citations
  5. D. Brinza and A. Zelikovsky, “2SNP: Scalable Phasing Method for Trios and Unrelated Individuals,” IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 6(1), pp. 313-318  (.pdf)  citations
  6. I. I. Mandoiu and A.Zelikovsky, “Preface,” in  Bioinformatics Algorithms: Techniques and Applications, I.I. Mandoiu and A. Zelikovsky (editors), Wiley Book Series on Bioinformatics, 2008, pp. ix-x. citations
  7. D. Brinza, J. He and A. Zelikovsky,  “Optimization Methods for Genotype Data Analysis in Epidemiological Studies,” in  Bioinformatics Algorithms: Techniques and Applications, I.I. Mandoiu and A. Zelikovsky (editors), Wiley Book Series on Bioinformatics, 2008, pp. 395- 415.   citations
  8. D. Brinza and A. Zelikovsky, “Design and Validation of Methods Searching for Risk Factors in Genotype Case-Control Studies,” RECOMB Satellite Workshop, SNPHAP 2007, January 27, 2007, (.ppt), Journal of Computational Biology, 15(1), 2008, pp. 81-90,  (.pdf)  citations
  9. G. Robins and A. Zelikovsky, “Minimum Steiner Tree Construction,” in The Handbook of Algorithms for VLSI Physical Design Automation, C.J. Alpert, D.P. Mehta, and S.S. Sapatnekar (editors), CRC Press, 2008, pp. 487-508.  citations

2007

  1. Q. Cheng, R. Harrison and A. Zelikovsky, “Mapping and Filling Metabolic Pathways,” Proc. RECOMB Satellite Conference on System Biology (RECOMB SCSB 2007).  citations
  2. 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, (.pdf)  citations
  3. 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. (.pdf)
  4. D. Brinza and A. Zelikovsky, “Risk Factor Searching Heuristics for SNP Case-Control Studies,” Proc. of IEEE International conference on Bioinformatics and Biomedicine (BIBM 2007), pp. 282 – 287. (.pdf) citations
  5. D. Brinza and A. Zelikovsky, “Discrete Methods for Association Search and Status Prediction in Genotype Case-Control Studies,” Proc. of IEEE 7-th International Symposium on BioInformatics and BioEngineering (BIBE'07), pp. 270-277. (.pdf)  citations
  6. 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'07), pp. 350-357. (.pdf) citations
  7. R. Albert, B. DasGupta, R. Dondi, E. Sontag, A. Zelikovsky and K. Westbrooks, “Signal Transduction Network Inference from Indirect Experimental Evidence,” Journal of Computational Biology, 14(7), 2007, pp. 927-949. (.pdf)  citations
  8. 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'07), September 2007, Lecture Notes in Bioinformatics (LNBI)  4645, pp. 407-419.  (.pdf)
  9. A.B. Kahng, I.I. Mandoiu, and A.Z. Zelikovsky, "Practical approximations of Steiner trees in uniform orientation metrics," in Handbook of Approximation Algorithms and Metaheuristics, T.E. Gonzalez, editor, Chapma&Hall/CRC Press, 2007, pp. 43-1 - 43-13. (.pdf)  citations
  10. I.I. Mandoiu, A. Olshevsky, and A.Z. Zelikovsky, "QoS multimedia multicast routing," in Handbook of Approximation Algorithms and Metaheuristics, T.E. Gonzalez, editor, Chapma&Hall/CRC Press, 2007, pp. 71-1 - 71-16. (.pdf)
  11. C. Albrecht, A.B. Kahng, I.I. Mandoiu and A.Z. Zelikovsky, "Multicommodity flow algorithms for buffered global routing," in Handbook of Approximation Algorithms and Metaheuristics, T.E. Gonzalez, editor, Chapma&Hall/CRC Press, 2007, pp. 80-1 - 80-18. (.pdf)
  12. I. Mandoiu and A. Zelikovsky, “Preface,” in Proceedings of International Symposium on Bioinformatics Research and Applications (ISBRA 2007), I. Mandoiu and A. Zelikovsky (eds.), Lecture Notes in Bioinformatics, LNBI 4463, Springer 2007, pp. v-x. (.pdf)
  13. N. Hundewale, S. Jung and A. Zelikovsky, “Energy Efficiency of Load Balancing in MANET Routing Protocols,” Journal of Universal Computer Science, 13(1), 2007, pp. 110-132. (.pdf) citations
  14. 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. (.pdf)
  15. J. He and A. Zelikovsky, “Informative SNP Selection Based on SNP Prediction,” IEEE Transactions on NanoBioscience, 6(1), 2007, pp. 60-67. (.pdf) citations
  16. I.I. Mandoiu, Yi Pan, and A. Zelikovsky, “Introduction to the Special Section on Computational Nanobioscience,” IEEE Transactions on NanoBioscience, 6(1), 2007, pp. 1-3. (.pdf)
  17. A. B. Kahng, I. I. Mandoiu, X. Xu and A. Zelikovsky, “Enhanced Design Flow and Optimizations for Multi-Project Wafers,” IEEE Transactions on CAD, 26(2), 2007, pp. 301-311.  (.pdf) citations
  18. 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 CAD, 26(1), 2007, pp.115-126. (.pdf) citations

2006

  1. 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, editors, Design Automation Methods and Tools for Microfluidics-Based Biochips. Springer Verlag, 2006, pp. 235-269. (.pdf)   citations
  2. D. Brinza and A. Zelikovsky, A. “Combinatorial Analysis of Disease Association and Susceptibility for Rheumatoid Arthritis SNP Data,” Proc. of Genetic Analysis Workshop (GAW15), November 2006 (.pdf)   citations
  3. 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 (GAW15), November 2006 (.pdf)    
  4. A. B. Kahng, P. Sharma, and A. Zelikovsky, “Fill for Shallow Trench Isolation CMP,” Proc. IEEE/ACM Intl Conf on Computer-Aided Design (ICCAD'06) November 2006, pp. 661-668 (.pdf)   citations
  5. D. Brinza  and A. Zelikovsky, “Combinatorial Methods for Disease Association Search and Susceptibility Prediction,” Proc. Workshop on Algorithms in Bioinformatics (WABI'06), September 2006, Lecture Notes in Bioinformatics (LNBI)  4175, pp. 286-297.  (.pdf) (.ppt)   citations
  6. D. Brinza, J. He, and A. Zelikovsky, “Combinatorial Search Methods for Multi-SNP Disease Association,” Proc. Intl Conf of the IEEE Engineering in Medicine and Biology (EMBC'06), September 2006, 5802-5805. (.pdf) (.ppt)   citations
  7. J.He and A. Zelikovsky, “Multiple Linear Regression for Index SNP Selection on Unphased Genotypes,” Proc. Intl Conf of the IEEE Engineering in Medicine and Biology (EMBC'06), September 2006, pp. 5759-5762. (.pdf) citations
  8. J. He and A. Zelikovsky, “MLR-Tagging: Informative SNP Selection for Unphased Genotypes Based on Multiple Linear Regression,” Bioinformatics, 22(20), 2006, pp. 2558–2561, (.pdf) citations
  9. Q. Cheng, Y. Zhang, X. Hu, N. Hundewale and A. Zelikovsky , “Routing Using Messengers in Sparse and Disconnected Mobile Sensor Networks,” Studies in Computational Intelligence, Volume 23 (2006), pp. 31-40 citations
  10. C. Albrecht, A.B. Kahng, I.I. Mandoiu, and A.Z. Zelikovsky, “Floorplan evaluation, global routing, and buffer insertion for integrated circuits,” United States Patent #7,062,743, June 2006. (.pdf)  citations
  11. D. Brinza, A. Perelygin, M. Brinton, A. Zelikovsky, “Search for multi-SNP Disease Association,” Proc. of the 5th Intl Conf on Bioinformatics of Genome Regulation and Structure (BGRS'2006), pp. 122-125. (.pdf) (.ppt)  citations
  12. D. Brinza and A. Zelikovsky, “DEEPS: Deterministic Energy-Efficient Protocol for Sensor networks,” Proc. 2nd ACIS Intl Workshop on Self-assembling Wireless Networks, (SAWN 2006), June 2006, pp. 261-266. (.pdf) (.ppt)   citations
  13. A. Dhawan, C. T. Vu, A. Zelikovsky, Y. Li, S. K. Prasad, “Maximum Lifetime of Sensor Networks with Adjustable Sensing Range,” Proc. 2nd  ACIS Intl Workshop on Self-assembling Wireless Networks, (SAWN 2006), June 2006, 285-289. (.pdf) (.ppt)   citations
  14. 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), pp. 287-299, 2006  (.ps), (.pdf)   citations
  15. D. Brinza and A. Zelikovsky, “Phasing of 2-SNP Genotypes based on Non-Random Mating Model,” Proc. of Intl Conf on Computational Science (ICCS 2006), May 2006, LNCS 3992, pp. 767-774. (.pdf) (.ppt)  citations
  16. J. He and A. Zelikovsky, “Tag SNP Selection Based on Multivariate Linear Regression,” Proc. of Intl Conf on Computational Science (ICCS 2006), May 2006, LNCS 3992, pp. 750-757. (.pdf) (.ppt)  citations
  17. 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 (GRC 2006), May 2006, pp. 754-757. (.pdf)  (.ppt)   citations
  18. J. He, J. Zhang, G. Altun, A. Zelikovsky and Y. Zhang, “Haplotype Tagging using Support Vector Machines,” Proc. IEEE Intl Conf on Granular Computing (GRC 2006), May 2006, pp. 758-761. (.pdf)   citations
  19. 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 (GRC 2006), May 2006, pp. 762-765. (.pdf)  citations
  20. 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), June 2006, LNCS 3967, pp. 70-79.  (.pdf)   citations
  21. A. B. Kahng, X. Xu and A. Zelikovsky, " Fast Yield-Driven Fracture for Variable Shaped-Beam Mask Writing," Proc. SPIE Symposium on Photomask and NGL Mask Technology XIII (Photomask Japan), April  2006, (Morihisa Hoga  ed.) Vol. 6283, 62832R, (2006), pp. 2R-1 - 2R-10.  (.pdf)   citations
  22. 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 Multiconf (SpringSim’06), April 2006, pp. 57-64. (.pdf)   citations
  23. 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 CAD, 25(2), February 2006, pp.305-320. (.pdf) citations
  24. D. Brinza and A. Zelikovsky, "2SNP: Scalable Phasing Based on 2-SNP Haplotypes," Bioinformatics, 22(3), 2006, pp. 371-373. (.pdf) Best Poster Award at the Fifth Georgia Tech International Conference on Bioinformatics, November 2005. citations
  25. 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 (EMLC 2006), January 2006, pp. 45-54. Invited (.pdf) citations

2005

  1. A. Zelikovsky, “Preface,” in Transactions on Computational Systems Biology II, C. Priami and A. Zelikovsky (eds.), LNBI 3680, Springer 2005, pp. v-vi.   citations
  2. 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 (MASS 2005), pp. 167-169. (.pdf)   citations
  3. 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, October 2005, Proceedings of SPIE 5992, pp. 1247-1257. Best Poster Award. (.pdf)   citations
  4. W. Mao, J.He, D. Brinza and A. Zelikovsky, "A Combinatorial Method for Predicting Genetic Susceptibility to Complex Diseases " Proc. Intl Conf of the IEEE Engineering in Medicine and Biology (EMBC'05), September 2005, pp. 224 - 227. (.pdf)    
  5. J. He, K. Westbrooks and A. Zelikovsky, "Linear Reduction Methods for Tag SNP Selection," International Journal on Bioinformatics Research and Applications 1(3), 2005, pp. 249-260. (.pdf)   citations
  6. D. Brinza, J. He, W. Mao and A. Zelikovsky, "Family Trio Phasing and Missing Data Recovery," International Journal on Bioinformatics Research and Applications, 1(2), 2005, pp. 221-229. (.pdf)  citations
  7. Y. Chen, A. B. Kahng, G. Robins, A. Zelikovsky and Y. Zheng, "Compressible Area Fill Synthesis," IEEE Transactions on CAD, 24(8), August 2005, pp. 1169- 1187. (.ps), (.pdf)   citations
  8. S. Jung, N. Hundewale and A. Zelikovsky, "Energy Efficiency of Load Balancing in MANET Routing Protocols," Proc. 1 ACIS Intl Workshop on Self-assembling Wireless Networks, (SAWN 2005), pp. 476-483. (.pdf)  citations
  9. D. Brinza, J. He, W. Mao and A. Zelikovsky, "Phasing and Missing data recovery in Family Trios," Proc. of Intl Conf on Computational Science (ICCS 2006), LNCS 3515, pp. 1011-1019.  (.pdf)   citations
  10. G. Calinescu and A. Zelikovsky, "The Polymatroid Steiner Problems," Journal of Combinatorial Optimization 9(3), May 2005, pp. 281-294. (.pdf)   citations
  11. G. Robins and A. Zelikovsky, "Tighter Bounds for Graph Steiner Tree Approximation," SIAM Journal on Discrete Mathematics, 19(1), March 2005, pp. 122-134. (.pdf), SIAM Outstanding Paper Prize Awarded in 2007   citations
  12. C. Chiang, A. B. Kahng, S. Sinha, X. Xu, and A. Zelikovsky, "Bright-Field AAPSM Conflict Detection and Correction," Proc. IEEE Conf on Design Automation and Test in Europe (DATE'05), Volume 2. March 2005, pp. 908-913. (.pdf)  citations
  13. S. Jung, N. Hundewale and A. Zelikovsky, "Node Caching Enhancement of Reactive Ad Hoc Routing Protocols," Proc. IEEE Wireless Communication and Networking Conference (WCNC'05), March 2005, Volume 4, 1970- 1975. (.pdf)  citations
  14. M. Karpinski, I. Mandoiu, A. Olshevsky and A. Zelikovsky, "Improved Approximation Algorithms for the Quality of Service Steiner Tree Problem," Algorithmica, 42(2) , April 2005, pp. 109-120. (.pdf)   citations
  15. 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, Volume 2, Y. Xiao and Y. Pan (Eds.), Nova Science Publishers. 2005. (.pdf)  citations
  16. D. D. Lozovanu, D. Solomon and A Zelikovsky, " Multiobjective Games and Determining Pareto-Nash Equilibria," Buletinul Academiei de Stiinte a Republicii Moldova, Math, N 3(49), 2005, pp. 115- 122. citations 

2004

  1. Y. Chen, A. B. Kahng, G. Robins, A. Zelikovsky and Y. Zheng, "Evaluation of the New OASIS Format for Layout Fill Compression," Proc. 11th IEEE Intl Conf on Electronics, Circuits and Systems (ICECS 2004), December 2004, 377-382. (.pdf), (.ppt)   citations
  2. 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, September 2004, Proceedings of  SPIE 5567, pp. 360-371. (.pdf)   citations
  3. G. Calinescu and A. Zelikovsky, "The Polymatroid Steiner Problems," Proc. of 15th Intl Symp on Algorithms and Computation, ISAAC 2004, December 2004, LNCS 3341, 234-245 (.pdf)  citations
  4. 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, 352-371. (.pdf)   citations
  5. J. He and A. Zelikovsky, "Linear Reduction for Haplotype Inference," Proc. Workshop on Algorithms in Bioinformatics (WABI'04), September 2004, Lecture Notes in Bioinformatics (LNBI) 3240, 242-253. (.pdf), (presentation)   citations
  6. M. Atlas, N. Hundewale, L. Perelygina and A. Zelikovsky, "Consolidating Software Tools for DNA Microarray Design and Manufacturing," Proc. Intl Conf of the IEEE Engineering in Medicine and Biology (EMBC'04), September 2004, 172-175. (.pdf), (presentation)  citations
  7. J. He and A. Zelikovsky, "Linear Reduction Methods for Tag SNP Selection," Proc. Intl Conf of the IEEE Engineering in Medicine and Biology (EMBC'04), September 2004, 2840-2843. (.pdf), (presentation) Regional Finalist for the Best Student Paper Award.   citations
  8. 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(2-3) March 2004, pp. 429-448. (.ps), (.pdf)  citations
  9. A. B. Kahng, I. Mandoiu, X. Xu and A. Zelikovsky, "Multi-Project Reticle Floorplanning and Wafer Dicing," Proc. IEEE/ACM Intl Symp on Physical Design, April 2004, pp. 70-77. (.pdf), (.ppt)  citations
  10. P. Berman, G. Calinescu, C. Shah and A. Zelikovsky, "Power Efficient Monitoring Management in Sensor Networks," IEEE Wireless Communication and Networking Conf (WCNC'04), Atlanta, March 2004, pp. 2329-2334. (.pdf), (presentation)  citations
  11. G. Calinescu, I. Mandoiu, P.-J. Wan and A. Zelikovsky, "Selecting Forwarding neighbors in Wireless Ad Hoc Networks," ACM Mobile Networks and Applications, 9(2), April 2004, pp. 101-111. (.ps), (.pdf)  citations

2003

  1. G. Calinescu, C. Fernandes, I. Mandoiu, A. Olshevsky, K. Yang and A. Zelikovsky, "Primal-Dual Algorithms for QoS Multimedia Multicast," Proc. of IEEE GLOBECOM 2003, December 2003, pp. 3631-3635. (.ps), (.pdf), (.ppt)   citations
  2. 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," IEEE Intl Workshop on Web Based Systems and Applications (WEBSA), in conjunction with the 27th Annual International Computer Software and Applications Conference (COMPSAC 2003), Dallas, Texas, November 3 - 6, 2003, pages 696-701. (.pdf)  citations
  3. 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'03) November 2003, pp. 262-269. (.ps), (.pdf), (.ppt)   citations
  4. 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 (ICCD2003), October 2003, pp. 116-123. (.ps), (.pdf), (.ppt)
  5. C. H. Helvig, G. Robins and A. Zelikovsky, "Moving-Target TSP and Related Problems," Journal of Algorithms, 49 (2003) pp. 153-174. (.ps), (.pdf)  citations
  6. G. Calinescu, S. Kapoor, A. Olshevsky and A. Zelikovsky, "Network Lifetime and Power Assignment in Ad-Hoc Wireless Networks," Proc. of European Symp on Algorithms (ESA'03), September 2003, LNCS 2832, pp. 114-126. (.ps), (.pdf)  citations
  7. M. Karpinski, I. Mandoiu, A. Olshevsky and A. Zelikovsky, "Improved Approximation Algorithms for the Quality of Service Steiner Tree Problem," Workshop on Algorithms and Data Structures (WADS), August 2003, LNCS 2748, pp. 401-411. (.ppt), (.ps), (.pdf)  citations
  8. C. Albrecht, A. B. Kahng, B. Liu, I. I . Mandoiu and A. Zelikovsky, "On the Skew-Bounded Minimum-Buffer Routing Tree Problem," IEEE Transactions on CAD, 22(7), 2003, pp. 937-944. (.ps), (.pdf)  citations
  9. G. Calinescu, C. G. Fernandes, H. Karloff and A. Zelikovsky, "A new approximation algorithm for finding heavy planar subgraphs," Algorithmica, 36 (2003) pp. 179-205. (.ps), (.pdf)  citations
  10. A. B. Kahng, I. Mandoiu, P. Pevzner, S. Reda and A. Zelikovsky, "Engineering a scalable placement heuristic for DNA probe arrays," Proc. the 7th Annual Intl Conf on Research in Computational Molecular Biology (RECOMB'03), Berlin, Germany, April 2003, pp. 148-156. (.ps), (.pdf), (.ppt)  citations
  11. E. Althaus, G. Calinescu, I. Mandoiu, S. Prasad, N. Tchervenski and A. Zelikovsky, "Power Efficient Range Assignment in Ad-hoc Wireless Networks," IEEE Wireless Communication and Networking Conf (WCNC'03), New Orleans, March 2003, pp. 1889-1894. (.ps), (.pdf), (.ppt), (cumberland-presentation), (poster) citations
  12. 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 CAD, 22(3), 2003, pp. 241-253. (.ps), (.pdf)  citations
  13. 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 (ASPDAC'03), January 2003, pp. 827-833 (.ps), (.pdf)  citations
  14. Y. Chen, A. B. Kahng, G. Robins, A. Zelikovsky and Y. Zheng, "Data Volume Reduction in Dummy Fill Generation," Proc. Conf. on Design Automation and Test in Europe (DATE'03), Munich, Germany, March 2003, pp. 868-873. (.ps)(.pdf)  citations

2002

  1. S.K. Prasad, M. Weeks, Y.-Q. Zhang, A. Zelikovsky, S. Belkasim and R. Sunderraman, "Mobile Fleet Application Using SOAP and System on Devices (SyD) Middleware Technologies," Proc. IASTED Communications, Internet and Info Tech (CIIT) Conf, November, 2002, 426-431.  citations
  2. Y. Chen, A. B. Kahng, G. Robins and A. Zelikovsky, "Area Fill Synthesis for Uniform Layout Density," IEEE Transactions on CAD, 21(10), 2002, pp. 1132-1147. (.ps), (.pdf)   citations
  3. 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'02), September 2002, LNCS 2452, pp. 435-448. (.ps), (.pdf), (presentation)   citations
  4. G. Calinescu, I. Mandoiu and A. Zelikovsky, "Symmetric Connectivity with Minimum Power Consumption in Radio Networks," Proc. 17th IFIP World Computer Congress, Stream TC1/ 2nd IFIP Intl Conf on Theoretical Computer Science (TCS 2002), R. Baeza-Yates and U. Montaniri and N. Santoro (eds.), Kluwer Academic Publ., August 2002, pp. 119-130. (.ps), (.pdf), (presentation), (poster)   citations
  5. C. Bandela, Y. Chen, A. B. Kahng, I. Mandoiu and A. Zelikovsky, "Auctions with buyer preferences," Information Systems: the E-BUsiness Challenge -- Proc. 17th IFIP World Computer Congress, Stream TC8, R. Traunmuller (ed.), Kluwer Academic Publ., August 2002, 223-238. (.pdf), (presentation)   citations
  6. Y. Chen, A. B. Kahng, G. Robins and A. Zelikovsky, "Smoothness and Uniformity of Filled Layout for VDSM Manufacturability," Proc. ACM/IEEE Intl Symp on Physical Design, April 2002, pp. 137-142. (.pdf), (presentation), (poster)   citations
  7. Y. Chen, A. B. Kahng, G. Robins and A. Zelikovsky, "Monte-Carlo Methods for Chemical-Mechanical Planarization on Multiple-Layer and Dual-Material Models," Proc. Intl Symp on Microlithography, March 2002, Proceedings of SPIE 4962, pp. 421-432. (.ps)   citations
  8. 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 CAD, 21(3), (2002), pp. 263-274. (.ps), (.pdf)   citations
  9. D. Lozovanu, V. Voloshin and A. Zelikovsky, "A note on the colorability of a mixed hypergraph using k colors," Comput. Sci. J. Moldova, 10, N.1(28), 2002, pp. 92-95.  
  10. D. D. Lozovanu, E. Tataru and A Zelikovsky, "A generalization of the knapsack problem and finding the k-optimal tree in a weighted digraph," Buletinul Academiei de Stiinte a Republicii Moldova, Math, N 1(38), 2002, pp. 111-117.  
  11. C. Albrecht, A. B. Kahng, I. Mandoiu and A. Zelikovsky, "Floorplan Evaluation with Timing-Driven Global Wireplanning, Pin Assignment and Buffer/Wire Sizing," Proc. VLSI Design/Asia and South Pacific Design Automation Conf, January 2002, pp. 580-587. Best Paper Award. .ps, .pdf, Poster, .ppt.  citations

2001

  1. 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'01) November 2001, pp. 408-415. .ps, .pdf, Poster,.ppt   citations
  2. 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 (SASIMI'01) October 2001, pp. 250-256. .ps, .pdf.  
  3. F. Dragan, A. B. Kahng, I. Mandoiu, S. Muddu and A. Zelikovsky, "Practical Approximation Algorithms for Separable Packing Linear Programs," Workshop on Algorithms and Data Structures (WADS), August 2001, LNCS 2125, pp. 325-337. (.ps), (.pdf).  citations
  4. 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 July 2001, ACM Press, pp. 34-43. .ps, .pdf, .ppt
  5. A. Zelikovsky, "Bottleneck Steiner Tree Problems," in Encyclopedia of Optimization, C. A. Floudas and P. M. Pardalos eds., Volume 1, June 2001, Kluwer Academic Publishers, pp. 203-205. (.ps).  
  6. Y. Chen, A. B. Kahng, G. Robins and A. Zelikovsky, "Hierarchical Dummy Fill Synthesis for Process Uniformity," Proc. Asia and South Pacific Design Automation Conf, January 2001, pp. 139-144.  (.ps), (.pdf), (ppt).  citations
  7. F. Dragan, A. B. Kahng, I. Mandoiu, S. Muddu and A. Zelikovsky, "Provably good global buffering by multiterminal multicommodity flow approximation," Proc. Asia and South Pacific Design Automation Conf., January 2001, pp. 120-125. (.ps), (.pdf).  citations
  8. A. B. Kahng, S. Vaya and A. Zelikovsky, "New Graph Bipartizations for Double-Exposure, Bright Field Alternating Phase-Shift Mask Layout," Proc. Asia and South Pacific Design Automation Conf, January 2001, pp. 133-138. (.ps), (.pdf), (ppt).  citations
  9. A. Zelikovsky and I. Mandoiu, "Practical Approximation Algorithms for Zero- and Bounded-Skew Trees," Proc. of ACM/SIAM Simposium on Discrete Algorithms, January 2001, pp. 407-416. (.ps), (.pdf), (ppt). citations
  10. C. H. Helvig, G. Robins and A. Zelikovsky, "An Improved Approximation Scheme for the Group Steiner Problem," Networks 37(1) (2001) pp. 8-20. (.ps), (.pdf).  citations
  11. A. Zelikovsky and I. Mandoiu, "Practical Approximation Algorithms for Zero- and Bounded-Skew Trees," SIAM Journal on Discrete Mathematics, 15(1) (2001), pp. 97-111. (.ps)(.pdf)   citations

2000

  1. 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 Computer-Aided Design (ICCAD'00), November 2000, pp. 104-109. (.ps), (.pdf), (ppt).  citations
  2. C. H. Helvig, G. Robins and A. Zelikovsky, "New Approximation Algorithms for Routing with Multi-port Treminals," IEEE Trans. on CAD 19(10), (2000) pp. 1118-1128. (.ps), (.pdf).   citations
  3. 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) (2000), pp. 165-167. (.ps), (.pdf) citations
  4. Y. Chen, A. B. Kahng, G. Robins and A. Zelikovsky, "Practical Iterated Fill Synthesis for CMP Uniformity," Proc. Design Automation Conf(DAC’00), June 2000, pp. 671-674.  (.ps), (.pdf), (.ppt) citations
  5. 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 Trans. on CAD 19(2), (2000), pp. 175-187. (.ps), (.pdf) citations
  6. 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, Jan. 2000, pp. 523-528. (.ps), (.pdf).  citations
  7. G. Robins and A. Zelikovsky, "Improved Steiner Tree Approximation in Graphs," Proc. of ACM/SIAM Simposium on Discrete Algorithms (SODA'2000), January 2000, pp. 770-779. (.ps), (ppt).  citations
  8. P. Berman and A. Zelikovsky, "On 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, January, 2000, pp. 117-135. (.ps). website  citations

1999

  1. Y. Chen, A. B. Kahng, G. Qu and A. Zelikovsky, "On the Associative-Skew Clock Routing Problem," Proc. IEEE/ACM Intl Conf on Computer-Aided Design (ICCAD'99) November 1999, pp. 168-172. (.ps), (.pdf). citations
  2. A. E. Caldwell, A. B. Kahng, S. Mantik, I. L. Markov and A. Zelikovsky, "On Wirelength Estimations for Row-Based Placement," IEEE Trans. on CAD 18(9), (1999), pp. 1265-1278. (.ps), (.pdf)citations
  3. 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," Workshop on Algorithms and Data Structures (WADS), August 1999, LNCS 1663, pp. 25-36. (.ps), (.pdf)citations
  4. 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. ACM Intl Symp on Physical Design (ISPD), April 1999, pp. 121-126. (.ps), (.pdf), (slides)citations
  5. A. B. Kahng, G. Robins, A. Singh and A. Zelikovsky, "Filling Algorithms and Analyses for Layout Density Control," IEEE Trans. on CAD 18(4), (1999), pp. 445-462. (.ps), (.pdf).  citations
  6. A. B. Kahng, G. Robins, A. Singh and A. Zelikovsky, "New and Exact Filling Algorithms for Layout Density Control," Proc. IEEE Intl Conf on VLSI Design, January 1999, pp. 106-110. (.ps), (.pdf), (.ppt)citations
  7. A. B. Kahng, G. Robins, A. Singh and A. Zelikovsky, "New Multilevel and Hierarchical Algorithms for Layout Density Control," Proc. Asia and South Pacific Design Automation Conf, January 1999, pp. 221-224.Nominated for Best Paper Award. (.ps), (.pdf)citations
  8. A. B. Kahng, P. Tucker and A. Zelikovsky, "Optimization of Linear Placements for Wirelength Minimization with Free Sites," Proc. Asia and South Pacific Design Automation Conf, January 1999, pp. 241-244. Nominated for Best Paper Award. (.ps), (.pdf), (.ppt)citations
  9. M. Mani, A Zelikovsky, G. Bhatia and A. B. Kahng, "Traversing probabilistic Graphs," Tech. Rep. CS-990010, UCLA, CA, 18 pp. (.pdf)citations

1998

  1. A. B. Kahng, H. Wang and A. Zelikovsky, "Automated Layout and Phase Assignment Techniques for Dark Field Alternating PSM," Proc. 18th BACUS Symp on Photomask Technology and Management, September 1998, pp. 222-231. (.ps), (.pdf), (.ppt)citations
  2. A. B. Kahng, G. Robins, A. Singh, H. Wang and A. Zelikovsky, "Filling and Slotting: Analysis and Algorithms," Proc. ACM/IEEE Intl Symp on Physical Design, April 1998, pp. 95-102. (.ps), (.pdf), (.ppt)citations
  3. A. E. Caldwell, A. B. Kahng, S. Mantik, I. L. Markov and A. Zelikovsky, "On Wirelength Estimations for Row-Based Placement," Proc. ACM/IEEE Intl. Symp. on Physical Design, April 1998, pp. 4-11. (.ps), (.pdf), (.ppt)citations
  4. C. H. Helvig, G. Robins and A. Zelikovsky, "Improved Approximation Bounds for the Group Steiner Problem," Proc. Conf on Design Automation and Test in Europe, Paris, France, February, 1998, pp. 406-413. (.ps)  citations
  5. C. H. Helvig, G. Robins and A. Zelikovsky, "Moving-Target TSP and Related Problems," Proc. of European Symp on Algorithms (ESA'98), In Algorithms-ESA'98, G. Bilardi, G. F. Italiano, A. Pietracaprina and G. Pucci (eds.) LNCS 1461, pp. 453-464 (.ps)citations
  6. M. Karpinski and A. Zelikovsky, "Approximating Dense Cases of Covering Problems," Proc. of the DIMACS Workshop on Network Design: Connectivity and Facilites Location, Princeton University, NJ, April, 1997. DIMACS series in Disc. Math. and Theor. Comp. Sci. 40, 1998, pp. 169-178. (.ps) . citations
  7. P. Berman, M. Furer and A. Zelikovsky, "Applications of the Matroid Parity Problem to Approximating Steiner Trees," Tech. Rep. 980021, Computer Science Dept., UCLA, Los Angeles 1998, 12 pp. (.ps).  citations

1997

  1. M. Karpinski, G. Wirtgen and A. Zelikovsky, "An Approximation Algorithm for the Bandwidth Problem on Dense Graphs," Proc. of RALCOM'97, Santorini , 1997, pp. 1-14. (.ps), (.pdf).  citations
  2. C. D. Bateman, C. H. Helvig, G. Robins and A. Zelikovsky, "Provably-Good Routing Tree Construction with Multi-Port Terminals," Proc. ACM/IEEE Intl Symp on Physical Design, April 1997, pp. 96-102. (.ps) citations
  3. M. Karpinski and A. Zelikovsky, "New approximation algorithms for the Steiner tree problems," Journal of Combinatorial Optimization 1(1), 1997, pp. 47-65. (.ps) citations
  4. A. Zelikovsky, "A series of Approximation Algorithms for the Acyclic Directed Steiner Tree Problem," Algorithmica 18, 1997, pp. 99-110. (.ps)  citations
  5. U. Fossmeier, M. Kaufmann and A. Zelikovsky, "Faster approximation algorithms for the rectilinear Steiner tree problem," Discrete & Computational Geometry 18, 1997, pp. 93-109. (.pdf) .  citations

1994-1996

  1. A. Zelikovsky, "Better approximation bounds for the network and Euclidean Steiner tree problems,"(.ps), Tech. Rep. CS-96-06, University of Virginia, Charlottesville, VA, 5 pp.  citations
  2. A. Zelikovsky, "Improved approximation of maximum planar subgraph," Tech. Rep. CS-96-09, University of Virginia, Charlottesville, VA, 8 pp. (.ps) citations
  3. Hwan-Gue Cho and A. Zelikovsky, "Spanning closed trail and Hamiltonian cycle in grid graphs," Proc. of 6th Intl Symp on Algorithms and Computation, ISAAC '95, LNCS 1002, 1995, pp. 342-351. (.ps)  citations
  4. 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'94), In Algorithms and Computation. K. W. Ng et al (eds.) LNCS 762, 1994, pp. 533-542. (.ps), (.pdf).  citations

1991-1993

  1. A. Zelikovsky, "Later achievements in the Steiner tree approximations," Journal of Computer Science of Moldova 1 (1993), pp. 32-41.  citations
  2. A. Zelikovsky, "A faster approximation algorithm for the Steiner tree problem in graphs," Information Processing Letters 46 (1993), pp. 79-83. (.pdf).  publisher url  citations
  3. A. Zelikovsky, "An 11/6-approximation algorithm for the network Steiner problem," Algorithmica 9 (1993), pp. 463-470. (.pdf)citations
  4. U. Fößmeier, M. Kaufmann, and A. Zelikovsky, "Faster approximation algorithms for the rectilinear Steiner tree problem," Proc. of 4th International Symposium on Algorithms and Computation, ISAAC '93, LNCS 762, (1993), pp. 533-542. (.pdf).  url citations
  5. D. D. Lozovanu, and A. Zelikovsky, "Minimal and bounded trees," Tezele Congresului XVIII al Academiei Romano-Americane, Kishinev, (1993), pp. 25-26. citations
  6. A. Zelikovsky, "A minimum base of weighted k-polymatroids and the Steiner tree problem," In Integer Programming and Combinatorial Optimization. G. Rinaldi and L. A. Wolsey (eds.) Proceedings of Conf. (IPCO-3), April 1993, pp. 89-98. citations
  7. 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, Vol. 60, 1992, pp.  733-745. citations
  8. A. Zelikovsky, "An 11/6-Approximation Algorithm for the Steiner Problem on Graphs" Annals of Discrete Mathematics, Vol. 51, (1992), pp. 351-354,  publisher url   citations
  9. A. Zelikovsky, “The Steiner tree problem in graphs without optimal vertices,” Matematicheskie Issledovaniia 21:44-49 (1991). citations

1982-1990

  1.  A. Zelikovsky, “König's problem for Abelian permutation groups,” Izvestia Academii Nauk Byelorusskoi Academii Nauk 5:34-39 (1989). (in Russian)
  2.  A. Zelikovsky, "The solution of König's problem for Abelian permutation groups,” Proc. XIX All-union algebraic Conf, L'vov, part 2, (1989), pp. 98-99. (in Russian)
  3. A. Zelikovsky, “Graph transformation categories which reconstruct graphs up to isomorphism,” Matematicheskie Issledovaniia 76:24-29 (1984). (in Russian)
  4. A. Zelikovsky and Le Thuk Zuk, “The contraction categories of graphs,” Matematicheskie Issledovaniia 66:56-59 (1982). (in Russian)
  5.  A. Zelikovsky, “Graphs of particular contraction categories,” Matematicheskie Issledovaniia 66:50-55 (1982). (in Russian)