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Notice: The documents contained in this directory are included by contributing authors as a means of ensuring timely dissemination of scholarly and technical work on a non-commercial basis. Copyright and all rights therein are maintained by the authors or by other copyright holders, notwithstanding that these works are offered here electronically. It is understood that all persons copying this information will adhere to the terms and constraints invoked by each author's copyright. These works may not be reposted without the explicit permission of the copyright holder.

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2024

  1. F. Mohebbi, A. Zelikovsky, S. Mangul, G. Chowell, and P. Skums. Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks. Nature Communications 15 (1), 2838. publisher url 

2023

  1. A. Juyal, R. Hosseini, D. Novikov, M. Grinshpon, and A. Zelikovsky. Reconstruction of Viral Variants via Monte Carlo Clustering. Journal of Computational Biology 30(9), 1009-1018. publisher url 
  2. H. Saghaian, P. Skums, Y. Ionov and A. Zelikovsky.  Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire, In: X. Guo, et al. (eds.), Bioinformatics Research and Applications. ISBRA 2023. Lecture Notes in Bioinformatics 14248 pp. 214-226. publisher url
  3. H. Farooq, D. Novikov, A. Juyal and A. Zelikovsky.  Genetic Algorithm with Evolutionary Jumps. In: X. Guo, et al. (eds.), Bioinformatics Research and Applications. ISBRA 2023. Lecture Notes in Bioinformatics 14248 pp.453-463. publisher url
  4. B. Sahoo, T. Adeyeha, Z. Pinnix and A. Zelikovsky.  Exploring Racial Disparities in Triple-Negative Breast Cancer: Insights from Feature Selection Algorithms. In: X. Guo, et al. (eds.), Bioinformatics Research and Applications. ISBRA 2023. Lecture Notes in Bioinformatics 14248 pp. 487-497. publisher url
  5. Z. Tayebi, A. Juyal, A. Zelikovsky and M. Patterson.  Simulating tumor evolution from scDNA-seq as an accumulation of both SNVs and CNAs. In: X. Guo, et al. (eds.), Bioinformatics Research and Applications. ISBRA 2023. Lecture Notes in Bioinformatics 14248 pp. 530-540. publisher url
  6. B. Sahoo, Z. Pinnix and Aa Zelikovsky.  Deep Learning Reveals Biological Basis of Racial Disparities in Quadruple-Negative Breast Cancer. In: X. Guo, et al. (eds.), Bioinformatics Research and Applications. ISBRA 2023. Lecture Notes in Bioinformatics 14248 pp. 498-508. publisher url
  7. X. Guo, S. Mangul, M. Patterson, A. Zelikovsky (eds.), Bioinformatics Research and Applications.
    19th International Symposium, ISBRA 2023, Wrocław, Poland, October 9–12, 2023, Proceedings. Lecture Notes in Bioinformatics 14248, Springer 2023. publisher url
  8. Cai Z, Skums P, Zelikovsky A. Special Issue, Part I: 18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022). Journal of Computational Biology 30(8), 829-30, 2023 publisher url
  9. Cai Z, Skums P, Zelikovsky A. Special Issue, Part II: 18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022). Journal of Computational Biology 30(9), 949-50, 2023 publisher url
  10. Sahoo B, Ali S, Chen P-Y, Patterson M, Zelikovsky A. Assessing the Resilience of Machine Learning Classification Algorithms on SARS-CoV-2 Genome Sequences Generated with Long-Read Specific Errors. Biomolecules. 2023; 13(6):934. publisher url 
  11. F. Mohebbi, A. Zelikovsky, S. Mangul, G. Chowell, P. Skums. "Community structure and temporal dynamics of SARS-CoV-2 epistatic network allows for early detection of emerging variants with altered phenotypes," bioRxiv 2023.04.02.535277, url
  12. A. Gaber, I. Mandric, C. Nitirahardjo, H. Piontkivska, A. Hillhouse, D. Threadgill, A. Zelikovsky,  A. Rogovskyy. "Comparative transcriptome analysis of Peromyscus leucopus and C3H mice infected with the Lyme disease pathogen." Frontiers in Cell and Infection Microbiology (13), 1115350. 2023  publisher url
  13. B. Sahoo, Z. Pinnix, S. Sims, A. Zelikovsky,  "Identifying Biomarkers Using Support Vector Machine to Understand the Racial Disparity in Triple-Negative Breast Cancer," Journal of Computational Biology 30(4) , 502-517, 2023 publisher url
  14. S Ali, B Sahoo, A Zelikovsky, PY Chen, M Patterson, "Benchmarking machine learning robustness in covid-19 genome sequence classification," Scientific Reports 13 (1), 4154, 2023 publisher url
  15. Mukul S. Bansal, Ion I. Măndoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, and Alexander Zelikovsky.Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021). Journal of Computational Biology 30(4), 363-5, 2023 publisher url

2022

  1. Cai Z, Skums P, Zelikovsky A. Special Issue: 17th International Symposium on Bioinformatics Research and Applications (ISBRA 2021). Journal of Computational Biology 29(10) 2022 publisher url
  2. S. Ali, B. Sahoo, M. A. Khan, A. Zelikovsky, I. U. Khan and M. Patterson, "Efficient Approximate Kernel Based Spike Sequence Classification," IEEE/ACM Transactions on Computational Biology and Bioinformatics  (TCBB),  2022, Epub ahead of print. publisher url
  3. M.S. Bansal,  I. Mandoiu, M. Moussa, M. Patterson, S. Rajasekaran, P. Skums, A. Zelikovsky (eds.), Computational Advances in Bio and Medical Sciences - 11th International Conference, ICCABS 2021, virtual event, December 16-18, 2021, Revised Selected Papers. Lecture Notes in Bioinformatics 13254, Springer 2022. publisher url
  4. B. Sahoo, S. Sims, and A. Zelikovsky,  "An SVM Based Approach to Study the Racial Disparity in Triple-Negative Breast Cancer," In: M.S. Bansal, et al. (eds.), Computational Advances in Bio and Medical Sciences. ICCABS 2021. Lecture Notes in Bioinformatics 13254: 163-175,  publisher url
  5. K. Vats, O. Kruglov, B. Sahoo, V. Soman, J. Zhang , G.V. Shurin, U.R. Chandran, P. Skums, M.R. Shurin, A. Zelikovsky, W.J. Storkus, Y.L. Bunimovich,  "Sensory nerves impede the formation of tertiary lymphoid structures and development of protective anti-melanoma immune responses," Cancer Immunology Research  10 (9): 1141–54, (2022)  publisher url
  6. F. Zhao, P. Skums, A. Zelikovsky, E.L. Sevigny, M.H. Swahn, S.M. Strasser, Y. Wu, "Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms,"  IEEE/ACM Transactions on Computational Biology and Bioinformatics  (TCBB),  2022, 19(1):180-191. publisher url
  7. S. Knyazev, K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan, D. Deshpande, P. Baykal, Z. Comarova, A. Lu, Y. Porozov, T. I. Vasylyeva, J.O. Wertheim, B.T. Tierney, C.Y. Chiu, R. Sun, A. Wu, M.S. Abedalthagafi, V.M. Pak, S.H. Nagaraj, A.L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C.E. Mason, E. Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T. T.-Y. Lam, N.C. Wu, A. Zelikovsky, R. Knight, K.A. Crandall and S. Mangul, "Unlocking capacities of genomics for the COVID-19 response and future pandemics,"  Nature Methods 2022:374-380. publisher url
  8. Juyal, A., Hosseini, R., Novikov, D., Grinshpon, M., Zelikovsky, A. "Entropy Based Clustering of Viral Sequences." In: Bansal, M.S., Cai, Z., Mangul, S. (eds) Bioinformatics Research and Applications. ISBRA 2022. Lecture Notes in Bioinformatics 13760: 369-380,  publisher url  

2021

  1. Y. Ionov, P. Srivastava, I.I. Mandoiu, A.Z. Zelikovsky, “Cancer Specific Immunotherapeutic Targets Generated by Chemotherapeutic Drug Treatment,” United States Patent Application #17,287,448, 12/9/2021, url
  2. S. Ali,  B. Sahoo, N. Ullah,  A. Zelikovsky, M. Patterson, I. Khan, "A k-mer Based Approach for SARS-CoV-2 Variant Identification," In: Wei Y., Li M., Skums P., Cai Z. (eds) Bioinformatics Research and Applications. ISBRA 2021. Lecture Notes in Computer Science, 13064. Springer, 2021, 153-164. publisher url
  3. S. Knyazev, D. Novikov, M. Grinshpon, H. Singh, R. Ayayyla, V. Sarwal, R. Hoseini, P. Icer, P. Skums, E. Campbell, S. Mangul, A. Zelikovsky, "A Novel Network Representation of SARS-CoV-2 Sequencing Data," In: Wei Y., Li M., Skums P., Cai Z. (eds) Bioinformatics Research and Applications. ISBRA 2021. Lecture Notes in Computer Science, 13064. Springer, 2021, 165-175. publisher url
  4. S.K. Jha, I. Mandoiu, S. Rajasekaran, P. Skums, A. Zelikovsky " Special Issue: 10th International Computational Advances in Bio and Medical Sciences (ICCABS 2020)," Journal of Computational Biology,  2021, 1033-1034, publisher url
  5. A. Melnyk, F. Mohebbi, S. Knyazev, B. Sahoo, R. Hosseini, P. Skums,  A. Zelikovsky, M. Patterson "From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering," Journal of Computational Biology,  2021, 1113-1129,  publisher url
  6. D. Novikov, S. Knyazev, M. Grinshpon, P. Icer, P. Skums, A. Zelikovsky, "Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations," Journal of Computational Biology,  2021, 1130-1141, publisher url
  7. M. Alser, J. Rotman, D. Deshpande, K. Taraszka, H. Shi, P. Baykal, H. Yang, V. Xue, S. Knyazev, B. Singer, B. Balliu, D. Koslicki, P. Skums, A. Zelikovsky, C. Alkan, O. Mutlu, S. Mangul “Technology dictates algorithms: recent developments in read alignment,” Genome Biology 22(1):249, (2021) publisher url
  8. F. Rondel, R. Hosseini, B. Sahoo, S. Knyazev, I. Mandric, F. Stewart, I. I. Măndoiu, B. Pasaniuc, Y. Porozov, A. Zelikovsky, "Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data," Journal of Computational Biology 28(8):842-855,  2021  publisher url
  9. Knyazev S, Tsyvina V, Shankar A, Melnyk A, Artyomenko A, Malygina T, Porozov YB, Campbell EM, Switzer WM, Skums P, Mangul S, Zelikovsky A. Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction. Nucleic Acids Res. 2021 49(17):e102. publisher url
  10. S.K. Jha, I. Mandoiu, S. Rajasekaran, P. Skums, A. Zelikovsky (eds.), Computational Advances in Bio and Medical Sciences - 10th International Conference, ICCABS 2020, virtual event, December 10-12, 2020, Revised Selected Papers. Lecture Notes in Bioinformatics 12686, Springer 2021. publisher url
  11. A. Melnyk, F. Mohebbi, S. Knyazev, B. Sahoo, R. Hosseini, P. Skums, A. Zelikovsky, M. Patterson, "Clustering Based Identification of SARS-CoV-2 Subtypes," In: Jha S.K., et al (eds) Computational Advances in Bio and Medical Sciences. ICCABS 2020. Lecture Notes in Bioinformatics 12686. 127-141, publisher url
  12. Cai Z, Skums P, Porozov Y, Zelikovsky A. Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020). Journal of Computational Biology 28(8):745-746, 2021 publisher url
  13. Cai Z, Skums P, Porozov Y, Zelikovsky A. "Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020)," Journal of Computational Biology 28(7):636, 2021 publisher url
  14. S. Knyazev, L. Hughes, P. Skums, A. Zelikovsky, "Epidemiological data analysis of viral quasispecies in the next-generation sequencing era," Briefings in Bioinformatics 22(1):96-108, 2021 publisher url
  15. I.I. Mandoiu, T.M. Murali, G. Narasimhan, S. Rajasekaran, P. Skums, A. Zelikovsky, "Special Issue: 9th International Computational Advances in Bio and Medical Sciences (ICCABS 2019)." Journal of Computational Biology 28(2): 115-116,  2021 publisher url
  16. P. Baykal, J. Lara, Y. Khudyakov, A. Zelikovsky, P.Skums "Quantitative differences between intra-host HCV populations from persons with recently established and persistent infections," Virus Evolution 7(1): veaa103, 2021 publisher url

2020

  1. S. Basodi, P. Baykal, A. Zelikovsky, P. Skums, Y. Pan,  "Analysis of heterogeneous genomic samples using image normalization and machine learning," BMC Genomics 21(Suppl 6):405, 2020 publisher url
  2. A. Melnyk, S. Knyazev, F. Vannberg, L. Bunimovich, P. Skums, A. Zelikovsky, "Using earth mover's distance for viral outbreak investigations," BMC Genomics 21(Suppl 5):582, 2020  publisher url
  3. V. Tsyvina, A. Zelikovsky, S. Snir, P. Skums, "Inference of mutability landscapes of tumors from single cell sequencing data," PLoS Comput Biol. 16(11):e1008454, 2020  publisher url
  4. F. Rondel, R. Hosseini, B. Sahoo, S. Knyazev, I. Mandric, F. Stewart, I. I. Măndoiu, B. Pasaniuc, A. Zelikovsky, "Estimating Enzyme Participation in Metabolic Pathways for Microbial Communities from RNA-seq Data," Proc. of International Symposium on Bioinformatics Research & Applications (ISBRA), 2020, Lecture Notes in Bioinformatics 12304, 335-343 publisher url
  5. K.Mitchell, J.J.Brito, I.Mandric, Q.Wu, S.Knyazev, S.Chang, L.S.Martin, A.Karlsberg, E.Gerasimov, R.Littman, B.L.Hill, N.C.Wu, H.Yang, K.Hsieh, L.Chen, E.Littman, T.Shabani, G.Enik, D.Yao, R.Sun, J.Schroeder, E.Eskin, A.Zelikovsky, P.Skums, M.Pop, S.Mangul: "Benchmarking of computational error-correction methods for next-generation sequencing data," BCB 2020: 63:1
  6. I.I. Mandoiu, T. M. Murali, G. Narasimhan, S. Rajasekaran, P. Skums, A. Zelikovsky (eds.), Computational Advances in Bio and Medical Sciences - 9th International Conference, ICCABS 2019, Miami, FL, USA, November 15-17, 2019, Revised Selected Papers. Lecture Notes in Computer Science 12029, Springer 2020. publisher url
  7. K. Mitchell, JJ. Brito, I. Mandric, Q.Wu, S. Knyazev, S. Chang, LS. Martin, A. Karlsberg, E. Gerasimov, R. Littman,  BL. Hill, NC. Wu, H.Yang, K. Hsieh, L. Chen, E. Littman, T. Shabani, G. Enik, D. Yao,  Ren Sun, J. Schroeder,  E. Eskin, A. Zelikovsky, P. Skums, M. Pop, S. Mangul, "Benchmarking of computational error correction methods for next-generation sequencing data," Genome Biology 21:71, (2020)  publisher url
  8. Z. Cai, P. Skums, A. Zelikovsky, "Special Issue Preface: 15th International Symposium on Bioinformatics Research and Applications (ISBRA 2019)," Journal of Computational Biology 27(2): 131-132,  2020
    publisher url
  9.  I Mandric, HT Yang, N Strauli, D Montoya, J Rotman, W Van Der Wey, JR Ronas, B Statz, D Yao, A Zelikovsky, R Spreafico, S Shifman, N Zaitlen, M Rossetti, K. M Ansel, E Eskin, S Mangul, "Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing,"  Nature Communications 11: 3126 (2020)
    publisher url
  10. J.J. Brito, T. Mosqueiro, J. Rotman, V. Xue, D.J. Chapski, J. De la Hoz, P. Matias, L.S. Martin, A. Zelikovsky, M. Pellegrini, S. Mangul, "Telescope: an interactive tool for managing large-scale analysis from mobile devices," GigaScience 9(1), 2020, giz163, publisher url
  11. D Laehnemann, J Köster, E Szcureck, D McCarthy, S C Hicks, MD Robinson, C A Vallejos, N Beerenwinkel, KR Campbell, A Mahfouz, L Pinello, P Skums, A Stamatakis, CS-O Attolini, S Aparicio, J Baaijens, M Balvert, B de Barbanson, A Cappuccio, G Corleone, B Dutilh, M Florescu, V Guryev, R Holmer, K Jahn, TJ Lobo, EM Keizer, I Khatri, S M Kiełbasa, J O Korbel, A M Kozlov, T-H Kuo, BPF Lelieveldt, II Mandoiu, JC Marioni, T Marschall, F Mölder, A Niknejad, Ł Rączkowski, M Reinders, J de Ridder, A-E Saliba, A Somarakis, O Stegle, FJ Theis, H. Yang, A Zelikovsky, AC McHardy, BJ Raphael, SP Shah, A. Schönhuth "11 Grand challenges in single-cell data science," Genome Biology 21:31, 2020 publisher url
  12. P. Skums, A. Kirpich, P. Icer Baykal, A. Zelikovsky, G. Chowell, "Global transmission network of SARS-CoV-2: from outbreak to pandemic." medRxiv [Preprint]. url

2019

  1. Y. Khudyakov, I.I. Mandoiu, P. Skums, A. Zelikovsky, "Workshop on Computational Advances in Molecular Epidemiology," Proceedings of BCB 2019: 561 publisher url
  2. Z. Cai, P. Skums, A. Zelikovsky, "Special Issue Preface: 14th International Symposium on Bioinformatics Research and Applications (ISBRA 2018)," Journal of Computational Biology 26(8): 767-768,  2019
    publisher url
  3. I. Mandoiu, P.Skums, A. Zelikovsky, “Guest Editors’ Introduction to the Special Section on  Bioinformatics  Research and Applications,” IEEE/ACM Transactions on Computational Biology and Bioinformatics  (TCBB), 16(4) pp.  1362 - 1363 (2019) publisher url
  4. P. Skums, V. Tsyvina, A. Zelikovsky, "Inference of clonal selection in cancer populations using single-cell sequencing data," Bioinformatics 35(14): i398–i407, 2019 publisher url
  5. A.S. Rogovskyy,  S.E.C. Caoili, Y. Ionov, H. Piontkivska, K V. Tsyvina, P. Skums, A. Zelikovsky, S.D. Waghela,  "Delineating surface epitopes of Lyme disease pathogen targeted by highly protective antibodies of New Zealand White rabbits.", Infection and Immunity, IAI.00246-19, 2019 publisher url
  6. F. Zhao, P. Skums, A. Zelikovsky, E.L. Sevigny, M.H. Swahn, S.M. Strasser, Y. Wu, "Detecting Illicit Drug Ads in Google+ Using Machine Learning," Proc. of International Symposium on Bioinformatics Research  & Applications (ISBRA), 2019, Lecture Notes in Bioinformatics 11490, 171-179 publisher url
  7. M. Batool, A.E. Hillhouse, Y. Ionov, K.J. Kochan, F. Mohebbi, G. Stoica, D.W .Threadgill, A. Zelikovsky, S.D. Waghela, D. J. Wiener, A.S. Rogovskyy, "New Zealand White rabbits effectively clear Borrelia burgdorferi B31 despite the bacteria's functional vlsE antigenic variation system", Infection and Immunity, IAI.00164-19, 2019 publisher url
  8. S. Mangul, L. Martin, B. Hill, A. K. Lam, M. Distler, A. Zelikovsky, E. Eskin, J. Flint, "Systematic benchmarking of omics computational tools," Nature Communications 10:1393, 2019. publisher ur citations
  9. A. Zelikovsky, I. Mandric, P. Skums, I. Mandoiu, B. Pasaniuc and P. Srivastava “Abstract LB-214: Imputation of single cell cancer genotypes,” In: Proc. of AACR Ann Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-214.publisher url

2018

  1. D. Kim, R. N. Uma, A. Zelikovsky (Eds.),  Combinatorial Optimization and Applications - 12th International Conference, COCOA 2018, Atlanta, GA, USA, December 15-17, 2018, Proceedings. Lecture Notes in Computer Science 11346, Springer 2018. publisher url
  2. S. Sims, A. G. Longmire, D.S. Campo, S. Ramachandran, M. Medrzycki, L. Ganova-Raeva, Y. Lin, A. Sue, H. Thai, A. Zelikovsky, Y. Khudyakov,"Automated quality control for a molecular surveillance system," BMC Bioinformatics 19(Suppl. 11):358, 2018.  publisher url
  3.  V. Tsyvina, D.S. Campo, S. Sims, A. Zelikovsky, Y. Khudyakov, P. Skums,"Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants," BMC Bioinformatics 19(Suppl. 11):360, 2018.  publisher url
  4. Y. Khudyakov, I.I. Mandoiu, P. Skums, A. Zelikovsky, "ACM-BCB 2018 Computational Advances in Molecular Epidemiology (CAME) Chairs' Welcome," Proceedings of BCB 2018: 574 publisher url
  5. Y. Wu, P. Skums, A. Zelikovsky, D.C. Rendon, X. Liao, “Predicting Opioid Epidemic by Using Twitter Data” Proc. of International Symposium on Bioinformatics Research  & Applications (ISBRA), 2018, Lecture Notes in Bioinformatics 10847, pp. 314-318. publisher url
  6. K. Han, A.B. Kahng, C. Moyes, A. Zelikovsky, “A study of optimal cost-skew tradeoff and remaining suboptimality in interconnect tree constructions,” SLIP '18 Proc., Article No. 2., 2018, publisher url
  7. M. Batool, S.E.C. Caoili, L.J. Dangott, E. Gerasimov, Y. Ionov, H. Piontkivska, A. Zelikovsky, S.D. Waghela, A.S. Rogovskyy, "Identification of surface epitopes associated with protection against highly immune-evasive VlsE-expressing Lyme disease spirochetes", Infection and Immunity, 86(8):e00182-18, 2018 publisher url
  8. I. Mandric, S. Knyazev, A. Zelikovsky, "Repeat aware evaluation of scaffolding tools," Bioinformatics 34(15):2530-37,  2018 publisher url
  9. Z. Cai, P. Skums, A. Zelikovsky, "Special Issue Preface: 13th International Symposium on Bioinformatics Research and Applications (ISBRA 2017)," Journal of Computational Biology 25(3): 251-252, 2018. publisher url
  10. 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, Y. Khudyakov, "QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data," Bioinformatics 34(1):163-70, 2018. publisher url

2017

  1. O.Glebova, S. Knyazev, A. Melnyk, A. Artyomenko, Y. Khudyakov, A. Zelikovsky, P. Skums, "Inference of genetic relatedness between viral quasispecies from sequencing data," BMC Genomics, 18(Suppl. 10):918,2017.  publisher url
  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, I.I. Mandoiu, "Fast Bootstrapping-Based Estimation of Confidence Intervals of Expression Levels and Differential Expression from RNA-Seq Data," Bioinformatics, 33(20):3302-3304, 2017 pdf preprint, publisher url, bibtex
  4. E. Gerasimov, A. Zelikovsky, I. Mandoiu, Y. Ionov. "Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire," BMC Bioinformatics, 18(Suppl. 8):244, 2017.  publisher url
  5.  N. Yu, X. Guo, A. Zelikovsky, Y. Pan, "GaussianCpG: a gaussian model for detection of CpG island in human genome sequences," BMC Genomics, 18(Suppl. 4):392, 2017.  publisher url
  6. D. Jha, P. Skums, A. Zelikovsky, Y. Khudyakov, 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, 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, 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. Basodi, P. B. Icer, P. Skums, Y. Khudyakov, A. Zelikovsky, and Y. Pan, “Classification of HCV infections through sequence image normalization,” ICCABS 2017. publisher url,
  10. 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.
  11. R.W. Harrison, I. Mandoiu, 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)
  12. P. Skums, A. Zelikovsky, "Guest Editorial Introduction to the Special Issue on Bioinformatics Research and Applications," IEEE Transactions on NanoBioscience 16(2) (2017): 79-80.
  13. 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, 24(6):558-570, 2017,  publisher url
  14. A. Rogovskyy, D. Gillis, Y. Ionov, E. Gerasimov, A. Zelikovsky, "Antibody response to Lyme disease spirochetes in the context of VlsE-mediated immune evasion", Infection and Immunity, 85(1):e00890-16, 2017, publisher url

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, A.Z. Zelikovsky (Eds.), Computational Methods for Next Generation Sequencing Data Analysis, John Wiley & Sons, 2016,publisher url, bibtex
  4. P. Skums, A. Artyomenko, O. Glebova, S. Ramachandran, D. S. Campo, Z. Dimitrova, I.I. Mândoiu, A. Zelikovsky, 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, 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, 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, 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, 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, S. Al Seesi, M. Mathew, I. Mandric, A. Rodriguez, K. Bean, Q. Cheng, O. Glebova, I.I. Mandoiu, N.B. Lopanik, A. Zelikovsky, "Inferring metabolic pathway activity levels from RNA-Seq data," BMC Genomics: 17(Suppl 5):542, 2016, pdf preprint, bibtex
  11. J. He,  Y. Li, 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, 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, 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): 695-704, 2015 
  2. I. Mandric, A. Zelikovsky, "ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching," Bioinformatics, 31(16):2632-2638, 2015, (.pdf) publisher url,  bibtex, citations
  3. I. Mandric, 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, 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. publisher url,
  6. E. Nenastyeva, A. Zelikovsky, Y. Ionov, I. I. Mandoiu, "Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire,” ICCABS 2015. publisher url,
  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, I.I. Mandoiu, "Bootstrap-based differential gene expression analysis for RNA-Seq data without replicates," BMC Genomics 15(Suppl 8):S2 , 2014, publisher url, bibtex citations
  2. Z. Cai, A. Zelikovsky, 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, 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, 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, A. Zelikovsky, “Reconstruction of Influenza A Virus Variants from  PacBio Reads”, ICCABS 2014, pdf. publisher url bibtex
  7. I. Astrovskaya, N. Mancuso, B. Tork, S. Mangul, A. Artyomenko, P. Skums, L. Ganova-Raeva, I.I. Mandoiu, 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, 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, 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, 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 url, bibtex  citations
  2. P. Skums, N. Mancuso, A. Artyomenko, B. Tork, I.I. Mandoiu, Y. Khudyakov, 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, 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, A. Zelikovsky, Distributed Algorithms for TDMA Link Scheduling in Sensor Networks, International Journal of Networks and Computing 3(1), pp. 55-74, 2013,  publisher url, bibtex 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 url, bibtex

2012

  1. J. Lindsay, H. Salooti, A. Zelikovsky, 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 url, bibtex  citations
  2. ​S. Mangul, A. Caciula, S. Al Seesi, D. Brinza, A. Rouf Banda, R. Kanadia, I.I. Mandoiu, 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 preprint, publisher url, bibtex  citations
  3.  J. Chen, I. Măndoiu, R. Sunderraman, J. Wang, A. Zelikovsky,  “Guest Editors’ Introduction,”  BMC Bioinformatics 13 (Suppl10): S1 2012,  publisher url, bibtex
  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, A. Zelikovsky. “Maximum Series-Parallel Subgraph," Algorithmica 63, pp. 137-157, (2012) publisher url, bibtex  citations
  6. J. Chen, 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 url, bibtex   
  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 url, bibtex  citations
  8. N. Mancuso, B. Tork, P. Skums, L. Ganova-Raeva, I.I. Mandoiu, A. Zelikovsky, "Reconstructing viral quasispecies from NGS amplicon reads," In Silico Biology 11, pp. 237-249, 2012,  publisher url, bibtex  citations
  9. Mangul, A. Caciula, O. Glebova, I.I. Mandoiu, A. Zelikovsky,Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations, In Silico Biology 11, pp. 251-261, 2012,publisher url, bibtex citations

2011

  1. 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 url, bibtex citations
  2. S. Mangul, A. Caciula, I.I. Mandoiu, 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, ppt, publisher url, bibtex  citations
  3. N. Mancuso, B. Tork, I.I. Mandoiu, A. Zelikovsky, 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 url, bibtex  citations
  4. S. Mangul, I. Astrovskaya, M. Nicolae, B. Tork, I.I. Mandoiu, 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 preprint, publisher url, bibtex citations
  5. I. Astrovskaya, B. Tork, S. Mangul, K. Westbrooks, I.I. Mandoiu, P. Balfe, A. Zelikovsky, “Inferring Viral Quasispecies Spectra from 454 Pyrosequencing Reads,” BMC Bioinformatics 12(Suppl 6):S1, 2011,  pdf preprint, publisher url, bibtex  citations
  6. M. Nicolae, S. Mangul, I.I. Mandoiu, A. Zelikovsky, ”Estimation of alternative splicing isoform frequencies from RNA-Seq data”, Algorithms for Molecular Biology 6:9, 2011 pdf preprint, publisher url, bibtex  citations
  7. 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 url, bibtex
  8. M. Borodovsky, T. M. Przytycka, S. Rajasekaran, 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 url, bibtex
  9. Q. Cheng, 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 url, bibtex  citations

2010

  1. B. Pasaniuc, R. Garfinkel, I. Mandoiu, A. Zelikovsky, “Optimal Testing of Digital  Microfluidic  Biochips,”  INFORMS Journal of Computing, 23(4),  pp. 518-529, 2010, pdf preprint, publisher url, bibtex  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, 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, 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, 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, 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, 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, A. Zelikovsky, “Editorial,” International Journal of Sensor Networks, 6(1) (2009), pp. 1-2. (.pdf).  (url)
  3. I. Astrovskaya, 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, 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, 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, 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, A. Zelikovsky, “MetNetAligner: a web service tool for metabolic network alignments,” Bioinformatics, 25 (15):1989-1990, 2009.  citations 
  8. Q. Cheng, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, A. Zelikovsky, "The Polymatroid Steiner Problems," Journal of Combinatorial Optimization 9(3), May 2005, pp. 281-294. (.pdf)   citations
  11. G. Robins, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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,  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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, A. Zelikovsky, "An Improved Approximation Scheme for the Group Steiner Problem," Networks 37(1) (2001) pp. 8-20. (.ps), (.pdf).  citations
  11. A. Zelikovsky, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, A B. Kahng, "Traversing probabilistic Graphs," Tech. Rep. CS-990010, UCLA, CA, 18 pp. (.pdf). citations

1998

  1. A.B. Kahng, H. Wang, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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

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, 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, 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

1982-1992

  1. 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
  2. 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
  3. A. Zelikovsky, “The Steiner tree problem in graphs without optimal vertices,” Matematicheskie Issledovaniia 21:44-49 (1991). citations
  4. A. Zelikovsky, “König's problem for Abelian permutation groups,” Izvestia Academii Nauk Byelorusskoi Academii Nauk 5:34-39 (1989). (in Russian)
  5.  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)
  6. A. Zelikovsky, “Graph transformation categories which reconstruct graphs up to isomorphism,” Matematicheskie Issledovaniia 76:24-29 (1984). (in Russian)
  7. A. Zelikovsky, Le Thuk Zuk, “The contraction categories of graphs,” Matematicheskie Issledovaniia 66:56-59 (1982). (in Russian)
  8.  A. Zelikovsky, “Graphs of particular contraction categories,” Matematicheskie Issledovaniia 66:50-55 (1982). (in Russian)