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Ion I. Mandoiu
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2020 – today
- 2023
- [j61]Mukul S. Bansal
, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky:
Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021). J. Comput. Biol. 30(4): 363-365 (2023) - [j60]Sahar Al Seesi
, Anas Al-Okaily
, Tatiana Shcheglova, Elham Sherafat, Fahad Alqahtani, Adam T. Hagymasi
, Anupinder Kaur, Pramod Kumar Srivastava, Ion I. Mandoiu
:
GeNeo: A Bioinformatics Toolbox for Genomics-Guided Neoepitope Prediction. J. Comput. Biol. 30(4): 538-551 (2023) - 2022
- [j59]Saurav Dhar
, Chengchen Zhang, Ion I. Mandoiu
, Mukul S. Bansal
:
TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 230-242 (2022) - [e13]Mukul S. Bansal
, Ion I. Mandoiu
, Marmar Moussa
, Murray Patterson
, Sanguthevar Rajasekaran
, Pavel Skums
, Alexander Zelikovsky
:
Computational Advances in Bio and Medical Sciences: 11th International Conference, ICCABS 2021, Virtual Event, December 16-18, 2021, Revised Selected Papers. Lecture Notes in Computer Science 13254, Springer International Publishing 2022, ISBN 978-3-031-17530-5 [contents] - 2021
- [j58]Ion I. Mandoiu, T. M. Murali, Giri Narasimhan
, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
:
Special Issue: 9th International Computational Advances in Bio and Medical Sciences (ICCABS 2019). J. Comput. Biol. 28(2): 115-116 (2021) - [j57]Marmar Moussa
, Ion I. Mandoiu
:
SC1: A Tool for Interactive Web-Based Single-Cell RNA-Seq Data Analysis. J. Comput. Biol. 28(8): 820-841 (2021) - [j56]Filipp Rondel
, Roya Hosseini
, Bikram Sahoo, Sergey Knyazev, Igor Mandric, Frank Stewart, Ion I. Mandoiu, Bogdan Pasaniuc, Yuri Porozov
, Alexander Zelikovsky
:
Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data. J. Comput. Biol. 28(8): 842-855 (2021) - [j55]Sumit Kumar Jha
, Ion I. Mandoiu, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky
:
Special Issue: 10th International Computational Advances in Bio and Medical Sciences (ICCABS 2020). J. Comput. Biol. 28(11): 1033-1034 (2021) - [c79]Samuel Sledzieski, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal:
TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference. PSB 2021 - [e12]Sumit Kumar Jha
, Ion I. Mandoiu
, Sanguthevar Rajasekaran
, Pavel Skums
, Alex Zelikovsky
:
Computational Advances in Bio and Medical Sciences - 10th International Conference, ICCABS 2020, Virtual Event, December 10-12, 2020, Revised Selected Papers. Lecture Notes in Computer Science 12686, Springer 2021, ISBN 978-3-030-79289-3 [contents] - 2020
- [j54]Elham Sherafat, Jordan Force, Ion I. Mandoiu
:
Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy. BMC Bioinform. 21-S(18): 498 (2020) - [j53]Fahad Alqahtani
, Ion I. Mandoiu
:
Statistical Mitogenome Assembly with RepeaTs. J. Comput. Biol. 27(9): 1407-1421 (2020) - [c78]Marmar Moussa
, Ion I. Mandoiu
:
Computational Cell Cycle Analysis of Single Cell RNA-Seq Data. ICCABS 2020: 71-87 - [c77]Fahad Alqahtani
, Ion I. Mandoiu
:
Mitochondrial Haplogroup Assignment for High-Throughput Sequencing Data from Single Individual and Mixed DNA Samples. ISBRA 2020: 1-12 - [c76]Saurav Dhar, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal
:
TNet: Phylogeny-Based Inference of Disease Transmission Networks Using Within-Host Strain Diversity. ISBRA 2020: 203-216 - [c75]Filipp Rondel, Akram Sadat Hosseini
, Bikram Sahoo, Sergey Knyazev
, Igor Mandric, Frank Stewart, Ion I. Mandoiu, Bogdan Pasaniuc, Alex Zelikovsky
:
Estimating Enzyme Participation in Metabolic Pathways for Microbial Communities from RNA-seq Data. ISBRA 2020: 335-343 - [c74]Marmar Moussa
, Ion I. Mandoiu:
SC1: A Tool for Interactive Web-Based Single Cell RNA-Seq Data Analysis. ISBRA 2020: 389-397 - [e11]Ion I. Mandoiu
, T. M. Murali, Giri Narasimhan
, Sanguthevar Rajasekaran
, Pavel Skums
, Alexander Zelikovsky
:
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, ISBN 978-3-030-46164-5 [contents] - [e10]Zhipeng Cai
, Ion I. Mandoiu
, Giri Narasimhan
, Pavel Skums, Xuan Guo
:
Bioinformatics Research and Applications - 16th International Symposium, ISBRA 2020, Moscow, Russia, December 1-4, 2020, Proceedings. Lecture Notes in Computer Science 12304, Springer 2020, ISBN 978-3-030-57820-6 [contents]
2010 – 2019
- 2019
- [j52]Marmar Moussa
, Ion I. Mandoiu
:
Locality Sensitive Imputation for Single Cell RNA-Seq Data. J. Comput. Biol. 26(8): 822-835 (2019) - [j51]Ion I. Mandoiu
, Pavel Skums
, Alexander Zelikovsky
:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 16(4): 1362-1363 (2019) - [c73]Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
:
Workshop on Computational Advances in Molecular Epidemiology. BCB 2019: 561 - [c72]Fahad Alqahtani
, Ion I. Mandoiu:
SMART2: Multi-library Statistical Mitogenome Assembly with Repeats. ICCABS 2019: 184-198 - [i9]David Laehnemann
, Johannes Köster
, Ewa Szczurek, Davis J. McCarthy
, Stephanie C. Hicks
, Mark D. Robinson
, Catalina A. Vallejos
, Niko Beerenwinkel, Kieran R. Campbell, Ahmed Mahfouz
, Luca Pinello, Pavel Skums, Alexandros Stamatakis
, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens
, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh
, Maria Florescu
, Victor Guryev, Rens Holmer
, Katharina Jahn, Thamar Jessurun Lobo
, Emma M. Keizer, Indu Khatri
, Szymon M. Kielbasa
, Jan O. Korbel, Alexey M. Kozlov
, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu
, John C. Marioni
, Tobias Marschall
, Felix Mölder
, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder
, Antoine-Emmanuel Saliba
, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth:
12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 7: e27885 (2019) - 2018
- [c71]Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
:
ACM-BCB 2018 Computational Advances in Molecular Epidemiology (CAME) Chairs' Welcome. BCB 2018: 574 - [c70]Fahad Alqahtani
, Ion I. Mandoiu:
Statistical Mitogenome Assembly with Repeats. ICCABS 2018: 1 - [c69]Marmar Moussa
, Ion I. Mandoiu:
SC1: A web-based single cell RNA-seq analysis pipeline. ICCABS 2018: 1 - [c68]Marmar Moussa
, Ion I. Mandoiu:
Locality Sensitive Imputation for Single-Cell RNA-Seq Data. ISBRA 2018: 347-360 - [p2]Andrew B. Kahng, Ion I. Mandoiu, Alexander Zelikovsky:
Practical Approximations of Steiner Trees in Uniform Orientation Metrics. Handbook of Approximation Algorithms and Metaheuristics (1) 2018: 657-669 - [p1]Ion I. Mandoiu, Alex Olshevsky, Alexander Zelikovsky:
QoS Multimedia Multicast Routing. Handbook of Approximation Algorithms and Metaheuristics (2) 2018 - 2017
- [j50]Igor Mandric, Yvette Temate-Tiagueu, Tatiana Shcheglova, Sahar Al Seesi
, Alex Zelikovsky
, Ion I. Mandoiu:
Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data. Bioinform. 33(20): 3302-3304 (2017) - [j49]Ekaterina Gerasimov, Alex Zelikovsky
, Ion I. Mandoiu, Yurij Ionov:
Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire. BMC Bioinform. 18(8): 244:1-244:6 (2017) - [j48]Robert W. Harrison
, Ion I. Mandoiu, Alexander Zelikovsky
:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 14(3): 576-577 (2017) - [c67]Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
:
CAME 2017: 6th Workshop on Computational Advances in Molecular Epidemiology. BCB 2017: 775 - [c66]Igor Mandric
, Sergey Knyazev
, Cory Padilla, Frank Stewart, Ion I. Mandoiu, Alex Zelikovsky
:
Metabolic Analysis of Metatranscriptomic Data from Planktonic Communities. ISBRA 2017: 396-402 - 2016
- [c65]Tyler Daddio, Ion I. Mandoiu:
Pairing T Cell Receptor α and β sequences using pooling and min-cost flows. ICCABS 2016: 1 - 2015
- [j47]Pavel Skums, Alexander Artyomenko, Olga Glebova, Sumathi Ramachandran
, Ion I. Mandoiu
, David S. Campo, Zoya Dimitrova, Alex Zelikovsky
, Yuri Khudyakov:
Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling. Bioinform. 31(5): 682-690 (2015) - [j46]Mai Hamdalla, Sanguthevar Rajasekaran, David F. Grant, Ion I. Mandoiu:
Metabolic Pathway Predictions for Metabolomics: A Molecular Structure Matching Approach. J. Chem. Inf. Model. 55(3): 709-718 (2015) - [c64]Ekaterina Nenastyeva, Alex Zelikovsky
, Yurij Ionov, Ion I. Mandoiu:
Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire. ICCABS 2015: 1 - [e9]Robert W. Harrison, Yaohang Li, Ion I. Mandoiu:
Bioinformatics Research and Applications - 11th International Symposium, ISBRA 2015, Norfolk, VA, USA, June 7-10, 2015 Proceedings. Lecture Notes in Computer Science 9096, Springer 2015, ISBN 978-3-319-19047-1 [contents] - 2014
- [j45]Edward Hemphill, James Lindsay, Chih Lee, Ion I. Mandoiu
, Craig E. Nelson:
Feature selection and classifier performance on diverse bio- logical datasets. BMC Bioinform. 15(S-13): S4 (2014) - [j44]James Lindsay, Hamed Salooti, Ion I. Mandoiu
, Alexander Zelikovsky
:
ILP-based maximum likelihood genome scaffolding. BMC Bioinform. 15(S-9): S9 (2014) - [c63]Adrian Caciula, Olga Glebova, Alexander Artyomenko, Serghei Mangul, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky
:
Deterministic regression algorithm for transcriptome frequency estimation. ICCABS 2014: 1 - [c62]Igor Mandric
, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky
:
SILP3: Maximum likelihood approach to scaffolding. ICCABS 2014: 1 - 2013
- [j43]Pavel Skums, Nicholas Mancuso, Alexander Artyomenko, Bassam Tork, Ion I. Mandoiu
, Yuri Khudyakov, Alex Zelikovsky
:
Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows. BMC Bioinform. 14(S-9): S2 (2013) - [j42]Mai Hamdalla, Ion I. Mandoiu
, Dennis W. Hill
, Sanguthevar Rajasekaran, David F. Grant:
BioSM: Metabolomics Tool for Identifying Endogenous Mammalian Biochemical Structures in Chemical Structure Space. J. Chem. Inf. Model. 53(3): 601-612 (2013) - [j41]Lochana C. Menikarachchi, Dennis W. Hill, Mai Hamdalla, Ion I. Mandoiu
, David F. Grant:
In Silico Enzymatic Synthesis of a 400 000 Compound Biochemical Database for Nontargeted Metabolomics. J. Chem. Inf. Model. 53(9): 2483-2492 (2013) - [j40]Ion I. Mandoiu
, Jianxin Wang, Alexander Zelikovsky
:
Guest Editors' introduction to the special section on bioinformatics research and applications. IEEE ACM Trans. Comput. Biol. Bioinform. 10(6): 1345-1346 (2013) - [c61]Alexander Artyomenko, Nicholas Mancuso, Alex Zelikovsky
, Pavel Skums, Ion I. Mandoiu
:
kGEM: An EM-based algorithm for local reconstruction of viral quasispecies. ICCABS 2013: 1 - [c60]Adrian Caciula, Alex Zelikovsky
, Serghei Mangul, James Lindsay, Ion I. Mandoiu
:
Monte-Carlo Regression algorithm for isoform frequency estimation from RNA-Seq data. ICCABS 2013: 1 - [c59]Gabriel Ilie, Alex Zelikovsky
, Ion I. Mandoiu:
Reference assisted nucleic acid sequence reconstruction from mass spectrometry data. ICCABS 2013: 1 - [c58]James Lindsay, Craig E. Nelson, Ion I. Mandoiu:
Towards whole transcriptome deconvolution using single-cell data. ICCABS 2013: 1 - [c57]Nicholas Mancuso, Alexander Artyomenko, Alex Zelikovsky
, Pavel Skums, Ion I. Mandoiu
:
Estimation of viral population structure from amplicon-based reads. ICCABS 2013: 1 - [c56]Serghei Mangul, Sahar Al Seesi, Ion I. Mandoiu, Adrian Caciula, Alex Zelikovsky
, Dumitru Brinza:
Transcriptome assembly and quantification from Ion Torrent RNA-Seq data. ICCABS 2013: 1 - [c55]Pavel Skums, Olga Glebova, Alex Zelikovsky
, Ion I. Mandoiu, Yuri Khudyakov:
Optimizing pooling strategies for the massive next-generation sequencing of viral samples. ICCABS 2013: 1 - 2012
- [j39]Jianer Chen, Ion I. Mandoiu
, Raj Sunderraman, Jianxin Wang, Alexander Zelikovsky
:
Guest Editors' Introduction. BMC Bioinform. 13(S-10): S1 (2012) - [j38]Serghei Mangul, Adrian Caciula, Dumitru Brinza, Ion I. Mandoiu, Alex Zelikovsky
:
TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads. BMC Bioinform. 13(S-18): A11 (2012) - [j37]Nicholas Mancuso, Bassam Tork, Pavel Skums, Lilia Ganova-Raeva, Ion I. Mandoiu
, Alex Zelikovsky
:
Reconstructing viral quasispecies from NGS amplicon reads. Silico Biol. 11(5-6): 237-249 (2012) - [j36]Serghei Mangul, Adrian Caciula, Olga Glebova, Ion I. Mandoiu
, Alex Zelikovsky
:
Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations. Silico Biol. 11(5-6): 251-261 (2012) - [c54]James Lindsay, Hamed Salooti, Alexander Zelikovsky
, Ion I. Mandoiu
:
Scalable genome scaffolding using integer linear programming. BCB 2012: 377-383 - [c53]Mai Hamdalla, David F. Grant, Ion I. Mandoiu
, Dennis W. Hill, Sanguthevar Rajasekaran, Reda A. Ammar:
The use of graph matching algorithms to identify biochemical substructures in synthetic chemical compounds: Application to metabolomics. ICCABS 2012: 1-6 - [c52]James Lindsay, Ion I. Mandoiu
, Hamed Salooti, Alexander Zelikovsky
:
Poster: Accurate scaffolding of large genomes using integer programming and Non-Serial Dynamic Programming. ICCABS 2012: 1 - [c51]Nicholas Mancuso, Bassam Tork, Pavel Skums, Lilia Ganova-Raeva, Ion I. Mandoiu
, Alexander Zelikovsky
:
Workshop: A maximum likelihood method for quasispecies spectrum assembly. ICCABS 2012: 1 - [c50]Serghei Mangul, Adrian Caciula, Ion I. Mandoiu
, Alexander Zelikovsky
:
Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution. ICCABS 2012: 1 - [c49]Rachel J. O'Neill, Ion I. Mandoiu, Mazhar I. Khan, Craig Obergfell, Hongjun Wang, Andrew Bligh, Bassam Tork, Nicholas Mancuso, Alexander Zelikovsky
:
Workshop: Bioinformatics methods for reconstruction of Infectious Bronchitis Virus quasispecies from next generation sequencing data. ICCABS 2012: 1 - [c48]Sahar Al Seesi
, Ion I. Mandoiu
:
Workshop: Inference of allele specific expression levels from RNA-Seq data. ICCABS 2012: 1 - [e8]Sorin Istrail, Ion I. Mandoiu, Mihai Pop, Sanguthevar Rajasekaran, John L. Spouge:
IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012, Las Vegas, NV, USA, February 23-25, 2012. IEEE Computer Society 2012, ISBN 978-1-4673-1320-9 [contents] - [e7]Leonidas G. Bleris, Ion I. Mandoiu
, Russell Schwartz, Jianxin Wang:
Bioinformatics Research and Applications - 8th International Symposium, ISBRA 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings. Lecture Notes in Computer Science 7292, Springer 2012, ISBN 978-3-642-30190-2 [contents] - 2011
- [j35]Marius Nicolae, Serghei Mangul, Ion I. Mandoiu
, Alex Zelikovsky
:
Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms Mol. Biol. 6: 9 (2011) - [j34]Jorge Duitama
, Justin Kennedy, Sanjiv Dinakar, Yözen Hernández
, Yufeng Wu, Ion I. Mandoiu
:
Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads. BMC Bioinform. 12(S-1): S53 (2011) - [j33]Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu
, Peter Balfe
, Alex Zelikovsky
:
Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinform. 12(S-6): S1 (2011) - [j32]Bogdan Pasaniuc, Robert S. Garfinkel, Ion I. Mandoiu, Alexander Zelikovsky
:
Optimal Testing of Digital Microfluidic Biochips. INFORMS J. Comput. 23(4): 518-529 (2011) - [c47]Nicholas Mancuso, Bassam Tork, Pavel Skums, Ion I. Mandoiu
, Alexander Zelikovsky
:
Viral quasispecies reconstruction from amplicon 454 pyrosequencing reads. BIBM Workshops 2011: 94-101 - [c46]Serghei Mangul, Adrian Caciula, Ion I. Mandoiu
, Alexander Zelikovsky
:
RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes. BIBM Workshops 2011: 118-123 - [c45]Jorge Duitama, Pramod Kumar Srivastava, Ion I. Mandoiu
:
Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data. ICCABS 2011: 87-92 - [c44]Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alexander Zelikovsky
:
Poster: ViSpA: Viral spectrum assembling method. ICCABS 2011: 234 - [c43]James Lindsay, J. Zhang, T. Farnham, Y. Wu, Ion I. Mandoiu, Rachel J. O'Neill, Hamed Salooti, E. Bullwinkel, Alexander Zelikovsky
:
Poster: Scaffolding draft genomes using paired sequencing data. ICCABS 2011: 252 - [c42]Marius Nicolae, Ion I. Mandoiu:
Poster: Empirical comparison of protocols for sequencing-based gene and isoform expression profiling. ICCABS 2011: 256 - [c41]Rachel J. O'Neill, James Lindsay, Dawn Carone, Sahar Al Seesi, Thomas Heider, Ion I. Mandoiu, Andrew Pask:
Workshop: The utility of next generation sequencing for genome scale studies. ICCABS 2011: 272 - [c40]Marius Nicolae, Ion I. Mandoiu
:
Accurate Estimation of Gene Expression Levels from DGE Sequencing Data. ISBRA 2011: 392-403 - [c39]Serghei Mangul, Irina Astrovskaya, Marius Nicolae, Bassam Tork, Ion I. Mandoiu
, Alexander Zelikovsky
:
Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data. WABI 2011: 213-224 - [e6]Ion I. Mandoiu, Satoru Miyano, Teresa M. Przytycka, Sanguthevar Rajasekaran:
IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011, Orlando, FL, USA, February 3-5, 2011. IEEE Computer Society 2011, ISBN 978-1-61284-851-8 [contents] - 2010
- [j31]Ion I. Mandoiu
, Giri Narasimhan
, Yi Pan, Yanqing Zhang:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 7(4): 577-578 (2010) - [c38]Marius Nicolae, Serghei Mangul, Ion I. Mandoiu
, Alexander Zelikovsky
:
Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data. WABI 2010: 202-214 - [i8]Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky:
Estimation of alternative splicing isoform frequencies from RNA-Seq data. Structure Discovery in Biology: Motifs, Networks & Phylogenies 2010
2000 – 2009
- 2009
- [j30]Jin Jun, Paul Ryvkin, Edward Hemphill, Ion I. Mandoiu
, Craig E. Nelson:
The Birth of New Genes by RNA- and DNA-Mediated Duplication during Mammalian Evolution. J. Comput. Biol. 16(10): 1429-1444 (2009) - [j29]Ion I. Mandoiu
, Yi Pan, Raj Sunderraman, Alexander Zelikovsky
:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 6(2): 178-179 (2009) - [c37]Ion I. Mandoiu
:
Genotype and Haplotype Reconstruction from Low-Coverage Short Sequencing Reads. BICoB 2009: 52-53 - [c36]Bogdan Pasaniuc, Justin Kennedy, Ion I. Mandoiu
:
Imputation-Based Local Ancestry Inference in Admixed Populations. ISBRA 2009: 221-233 - [e5]Ion I. Mandoiu
, Giri Narasimhan, Yanqing Zhang:
Bioinformatics Research and Applications, 5th International Symposium, ISBRA 2009, Fort Lauderdale, FL, USA, May 13-16, 2009, Proceedings. Lecture Notes in Computer Science 5542, Springer 2009, ISBN 978-3-642-01550-2 [contents] - [i7]Justin Kennedy, Ion I. Mandoiu, Bogdan Pasaniuc:
GEDI: Scalable Algorithms for Genotype Error Detection and Imputation. CoRR abs/0911.1765 (2009) - 2008
- [j28]Justin Kennedy, Ion I. Mandoiu
, Bogdan Pasaniuc
:
Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity. J. Comput. Biol. 15(9): 1155-1171 (2008) - [j27]Alexander Gusev, Ion I. Mandoiu
, Bogdan Pasaniuc
:
Highly Scalable Genotype Phasing by Entropy Minimization. IEEE ACM Trans. Comput. Biol. Bioinform. 5(2): 252-261 (2008) - [j26]Ion I. Mandoiu
, Yi Pan, Alexander Zelikovsky
:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 5(3): 321-322 (2008) - [c35]Bhaskar DasGupta, Jin Jun, Ion I. Mandoiu:
Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP. APBC 2008: 353-362 - [c34]Sudha Balla, Sanguthevar Rajasekaran, Ion I. Mandoiu
:
Faster greedy algorithms for Multiple Degenerate Primer Selection. BIBE 2008: 1-4 - [c33]Jin Jun, Paul Ryvkin, Edward Hemphill, Ion I. Mandoiu
, Craig E. Nelson:
Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events during Mammalian Evolution. RECOMB-CG 2008: 40-54 - [e4]Ion I. Mandoiu
, Raj Sunderraman, Alexander Zelikovsky
:
Bioinformatics Research and Applications, Fourth International Symposium, ISBRA 2008, Atlanta, GA, USA, May 6-9, 2008. Proceedings. Lecture Notes in Computer Science 4983, Springer 2008, ISBN 978-3-540-79449-3 [contents] - [e3]Ion I. Mandoiu, Andrew A. Kennings:
The Tenth International Workshop on System-Level Interconnect Prediction (SLIP 2008), Newcastle, UK, April 5-8, 2008, Proceedings. ACM 2008, ISBN 978-1-59593-918-0 [contents] - 2007
- [j25]Sudha Balla, Sanguthevar Rajasekaran, Ion I. Mandoiu
:
Efficient Algorithms for degenerate Primer Search. Int. J. Found. Comput. Sci. 18(4): 899-910 (2007) - [j24]Gruia Calinescu, Ion I. Mandoiu, Alexander Zelikovsky, Marius Zimand:
Selected Papers from the 1st ACIS International Workshop on Self-Assembling Wireless Networks. J. Univers. Comput. Sci. 13(1): 1-3 (2007) - [j23]Andrew B. Kahng, Ion I. Mandoiu
, Xu Xu, Alexander Zelikovsky
:
Enhanced Design Flow and Optimizations for Multiproject Wafers. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 26(2): 301-311 (2007) - [j22]Ion I. Mandoiu
, Yi Pan, Alexander Zelikovsky
:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 4(4): 513-514 (2007) - [c32]Justin Kennedy, Ion I. Mandoiu, Bogdan Pasaniuc:
Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity. WABI 2007: 73-84 - [e2]Ion I. Mandoiu
, Alexander Zelikovsky
:
Bioinformatics Research and Applications, Third International Symposium, ISBRA 2007, Atlanta, GA, USA, May 7-10, 2007, Proceedings. Lecture Notes in Computer Science 4463, Springer 2007, ISBN 978-3-540-72030-0 [contents] - [e1]Andrew A. Kennings, Ion I. Mandoiu:
The Ninth International Workshop on System-Level Interconnect Prediction (SLIP 2007), Austin, Texas, USA, March 17-18, 2007, Proceedings. ACM 2007, ISBN 978-1-59593-622-6 [contents] - [r3]Ion I. Mandoiu, Andrew B. Kahng, Christoph Albrecht, Alexander Zelikovsky
:
Multicommodity Flow Algorithms for Buffered Global Routing. Handbook of Approximation Algorithms and Metaheuristics 2007 - [r2]Ion I. Mandoiu, Andrew B. Kahng, Alexander Zelikovsky
:
Practical Approximations of Steiner Trees in Uniform Orientation Metrics. Handbook of Approximation Algorithms and Metaheuristics 2007 - [r1]Ion I. Mandoiu, Alex Olshevsky, Alexander Zelikovsky:
QoS Multimedia Multicast Routing. Handbook of Approximation Algorithms and Metaheuristics 2007 - 2006
- [j21]Ion I. Mandoiu
, Dragos Trinca:
Exact and Approximation Algorithms for DNA Tag Set Design. J. Comput. Biol. 13(3): 732-744 (2006) - [j20]Andrew B. Kahng, Ion I. Mandoiu, Sherief Reda, Xu Xu, Alexander Zelikovsky
:
Computer-Aided Optimization of DNA Array Design and Manufacturing. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 25(2): 305-320 (2006) - [j19]Ernst Althaus, Gruia Calinescu, Ion I. Mandoiu
, Sushil K. Prasad
, N. Tchervenski, Alexander Zelikovsky
:
Power Efficient Range Assignment for Symmetric Connectivity in Static Ad Hoc Wireless Networks. Wirel. Networks 12(3): 287-299 (2006) - [c31]Bogdan Pasaniuc
, Ion I. Mandoiu
:
Highly Scalable Genotype Phasing by Entropy Minimization. EMBC 2006: 3482-3486 - [c30]Ion I. Mandoiu, Claudia Prajescu:
High-Throughput SNP Genotyping by SBE/SBH. International Conference on Computational Science (2) 2006: 742-749 - [c29]Mohammad Taghi Hajiaghayi, Kamal Jain, Lap Chi Lau, Ion I. Mandoiu
, Alexander Russell
, Vijay V. Vazirani:
Minimum Multicolored Subgraph Problem in Multiplex PCR Primer Set Selection and Population Haplotyping. International Conference on Computational Science (2) 2006: 758-766 - 2005
- [j18]Marek Karpinski, Ion I. Mandoiu, Alexander Olshevsky, Alexander Zelikovsky:
Improved Approximation Algorithms for the Quality of Service Multicast Tree Problem. Algorithmica 42(2): 109-120 (2005) - [j17]Bhaskar DasGupta, Kishori M. Konwar, Ion I. Mandoiu
, Alexander A. Shvartsman
:
DNA-BAR: distinguisher selection for DNA barcoding. Bioinform. 21(16): 3424-3426 (2005) - [j16]Bhaskar DasGupta, Kishori M. Konwar, Ion I. Mandoiu, Alexander A. Shvartsman
:
Highly scalable algorithms for robust string barcoding. Int. J. Bioinform. Res. Appl. 1(2): 145-161 (2005) - [j15]Hongyu Chen, Chung-Kuan Cheng, Andrew B. Kahng, Ion I. Mandoiu
, Qinke Wang, Bo Yao:
The Y architecture for on-chip interconnect: analysis and methodology. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 24(4): 588-599 (2005) - [j14]Puneet Gupta
, Andrew B. Kahng, Ion I. Mandoiu
, Puneet Sharma:
Layout-aware scan chain synthesis for improved path delay fault coverage. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 24(7): 1104-1114 (2005) - [j13]Ion I. Mandoiu, Claudia Prajescu, Dragos Trinca:
Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays. Trans. Comp. Sys. Biology 2: 124-137 (2005) - [c28]Kishori M. Konwar, Ion I. Mandoiu, Alexander Russell, Alexander A. Shvartsman:
Improved algorithms for multiplex PCR primer set selection with amplification length constraints. APBC 2005: 41-50 - [c27]Ion I. Mandoiu, Dragos Trinca:
Exact and Approximation Algorithms for DNA Tag Set Design. CPM 2005: 383-393 - [c26]Ion I. Mandoiu, Claudia Prajescu, Dragos Trinca:
Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays. International Conference on Computational Science (2) 2005: 994-1002 - [c25]Bhaskar DasGupta, Kishori M. Konwar, Ion I. Mandoiu, Alexander A. Shvartsman:
Highly Scalable Algorithms for Robust String Barcoding. International Conference on Computational Science (2) 2005: 1020-1028 - [i6]Ion I. Mandoiu, Claudia Prajescu, Dragos Trinca:
Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays. CoRR abs/cs/0502054 (2005) - [i5]Bhaskar DasGupta, Kishori M. Konwar, Ion I. Mandoiu, Alexander A. Shvartsman:
Highly Scalable Algorithms for Robust String Barcoding. CoRR abs/cs/0502065 (2005) - [i4]Ion I. Mandoiu, Dragos Trinca:
Exact and Approximation Algorithms for DNA Tag Set Design. CoRR abs/cs/0503057 (2005) - [i3]Christoph Albrecht, Andrew B. Kahng, Ion I. Mandoiu, Alexander Zelikovsky:
Multicommodity Flow Algorithms for Buffered Global Routing. CoRR abs/cs/0508045 (2005) - [i2]Ion I. Mandoiu, Claudia Prajescu:
High-Throughput SNP Genotyping by SBE/SBH. CoRR abs/cs/0512052 (2005) - 2004
- [j12]Andrew B. Kahng, Ion I. Mandoiu
, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky
:
Scalable Heuristics for Design of DNA Probe Arrays. J. Comput. Biol. 11(2/3): 429-447 (2004) - [j11]Gruia Calinescu, Ion I. Mandoiu
, Peng-Jun Wan, Alexander Zelikovsky
:
Selecting Forwarding Neighbors in Wireless Ad Hoc Networks. Mob. Networks Appl. 9(2): 101-111 (2004) - [j10]Andrew B. Kahng, Bao Liu, Ion I. Mandoiu
:
Nontree routing for reliability and yield improvement [IC layout]. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 23(1): 148-156 (2004) - [c24]Andrew B. Kahng, Ion I. Mandoiu, Qinke Wang, Xu Xu, Alexander Zelikovsky
:
Multi-project reticle floorplanning and wafer dicing. ISPD 2004: 70-77 - [i1]Kishori M. Konwar, Ion I. Mandoiu, Alexander Russell, Alexander A. Shvartsman:
Approximation Algorithms for Minimum PCR Primer Set Selection with Amplification Length and Uniqueness Constraints. CoRR cs.DS/0406053 (2004) - 2003
- [j9]Charles J. Alpert, Andrew B. Kahng, Bao Liu, Ion I. Mandoiu
, Alexander Zelikovsky
:
Minimum buffered routing with bounded capacitive load for slew rate and reliability control. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 22(3): 241-253 (2003) - [j8]Christoph Albrecht, Andrew B. Kahng, Bao Liu, Ion I. Mandoiu
, Alexander Zelikovsky
:
On the skew-bounded minimum-buffer routing tree problem. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 22(7): 937-945 (2003) - [c23]Andrew B. Kahng, Ion I. Mandoiu, Alexander Zelikovsky:
Highly scalable algorithms for rectilinear and octilinear Steiner trees. ASP-DAC 2003: 827-833 - [c22]Gruia Calinescu, Cristina G. Fernandes
, Ion I. Mandoiu, Alexander Olshevsky, K. Yang, Alexander Zelikovsky:
Primal-dual algorithms for QoS multimedia multicast. GLOBECOM 2003: 3631-3635 - [c21]Hongyu Chen, Chung-Kuan Cheng, Andrew B. Kahng, Ion I. Mandoiu, Qinke Wang, Bo Yao:
The Y-Architecture for On-Chip Interconnect: Analysis and Methodology. ICCAD 2003: 13-20 - [c20]Andrew B. Kahng, Ion I. Mandoiu, Sherief Reda, Xu Xu, Alexander Zelikovsky:
Evaluation of Placement Techniques for DNA Probe Array Layout. ICCAD 2003: 262-269 - [c19]Puneet Gupta, Andrew B. Kahng, Ion I. Mandoiu, Puneet Sharma:
Layout-Aware Scan Chain Synthesis for Improved Path Delay Fault Coverage. ICCAD 2003: 754-759 - [c18]Andrew B. Kahng, Ion I. Mandoiu, Sherief Reda, Xu Xu, Alexander Zelikovsky
:
Design Flow Enhancements for DNA Arrays. ICCD 2003: 116- - [c17]Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky
:
Engineering a scalable placement heuristic for DNA probe arrays. RECOMB 2003: 148-156 - [c16]Hongyu Chen, Chung-Kuan Cheng, Andrew B. Kahng, Ion I. Mandoiu, Qinke Wang:
Estimation of wirelength reduction for lambda-geometry vs. manhattan placement and routing. SLIP 2003: 71-76 - [c15]Marek Karpinski, Ion I. Mandoiu, Alexander Olshevsky, Alexander Zelikovsky:
Improved Approximation Algorithms for the Quality of Service Steiner Tree Problem. WADS 2003: 401-411 - [c14]Ernst Althaus, Gruia Calinescu, Ion I. Mandoiu, Sushil K. Prasad
, N. Tchervenski, Alexander Zelikovsky
:
Power efficient range assignment in ad-hoc wireless networks. WCNC 2003: 1889-1894 - 2002
- [j7]Kamal Jain, Ion I. Mandoiu
, Vijay V. Vazirani, David P. Williamson:
A primal-dual schema based approximation algorithm for the element connectivity problem. J. Algorithms 45(1): 1-15 (2002) - [j6]Feodor F. Dragan, Andrew B. Kahng, Ion I. Mandoiu
, Sudhakar Muddu, Alexander Zelikovsky
:
Provably good global buffering by generalized multiterminalmulticommodity flow approximation. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 21(3): 263-274 (2002) - [c13]Andrew B. Kahng, Bao Liu, Ion I. Mandoiu
:
Non-tree routing for reliability and yield improvement. ICCAD 2002: 260-266 - [c12]C. Bandela, Yu Chen, Andrew B. Kahng, Ion I. Mandoiu, Alexander Zelikovsky:
Auctions with Buyer Preferences. Information Systems: The e-Business Challenge 2002: 223-238 - [c11]Gruia Calinescu, Ion I. Mandoiu, Alexander Zelikovsky
:
Symmetric Connectivity with Minimum Power Consumption in Radio Networks. IFIP TCS 2002: 119-130 - [c10]Christoph Albrecht, Andrew B. Kahng, Ion I. Mandoiu, Alexander Zelikovsky:
Floorplan Evaluation with Timing-Driven Global Wireplanning, Pin Assignment and Buffer/Wire Sizing. ASP-DAC/VLSI Design 2002: 580- - [c9]Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky
:
Border Length Minimization in DNA Array Design. WABI 2002: 435-448 - 2001
- [j5]Alexander Zelikovsky
, Ion I. Mandoiu
:
Practical Approximation Algorithms for Zero- and Bounded-Skew Trees. SIAM J. Discret. Math. 15(1): 97-111 (2001) - [c8]Feodor F. Dragan, Andrew B. Kahng, Ion I. Mandoiu, Sudhakar Muddu, Alexander Zelikovsky
:
Provably good global buffering by multi-terminal multicommodity flow approximation. ASP-DAC 2001: 120-125 - [c7]Gruia Calinescu, Ion I. Mandoiu, Peng-Jun Wan, Alexander Zelikovsky:
Selecting forwarding neighbors in wireless Ad Hoc networks. DIAL-M 2001: 34-43 - [c6]Charles J. Alpert, Andrew B. Kahng, Bao Liu, Ion I. Mandoiu, Alexander Zelikovsky
:
Minimum-Buffered Routing of Non-Critical Nets for Slew Rate and Reliability Control. ICCAD 2001: 408- - [c5]Alexander Zelikovsky, Ion I. Mandoiu:
Practical approximation algorithms for zero- and bounded-skew trees. SODA 2001: 407-416 - [c4]Feodor F. Dragan, Andrew B. Kahng, Ion I. Mandoiu, Sudhakar Muddu, Alexander Zelikovsky
:
Practical Approximation Algorithms for Separable Packing Linear Programs. WADS 2001: 325-337 - 2000
- [j4]Ion I. Mandoiu
, Alexander Zelikovsky
:
A note on the MST heuristic for bounded edge-length Steiner trees with minimum number of Steiner points. Inf. Process. Lett. 75(4): 165-167 (2000) - [j3]Ion I. Mandoiu
, Vijay V. Vazirani, Joseph L. Ganley:
A new heuristic for rectilinear Steiner trees. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 19(10): 1129-1139 (2000) - [c3]Feodor F. Dragan, Andrew B. Kahng, Ion I. Mandoiu, Sudhakar Muddu, Alexander Zelikovsky
:
Provably Good Global Buffering Using an Available Buffer Block Plan. ICCAD 2000: 104-109
1990 – 1999
- 1999
- [c2]Ion I. Mandoiu, Vijay V. Vazirani, Joseph L. Ganley:
A new heuristic for rectilinear Steiner trees. ICCAD 1999: 157-162 - [c1]Kamal Jain, Ion I. Mandoiu, Vijay V. Vazirani, David P. Williamson:
A Primal-Dual Schema Based Approximation Algorithm for the Element Connectivity Problem. SODA 1999: 484-489 - 1998
- [j2]Ion I. Mandoiu:
Optimum Extensions of Prefix Codes. Inf. Process. Lett. 66(1): 35-40 (1998) - [j1]Kamal Jain, Ion I. Mandoiu
, Vijay V. Vazirani:
The 'Art of Trellis Decoding' Is Computationally Hardi - For Large Fields. IEEE Trans. Inf. Theory 44(3): 1211-1214 (1998)
Coauthor Index
aka: Alexander Zelikovsky
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