Ion I. Mandoiu

ORCID

Publication Activity (10 Years)

Years Active: 1998-2023
Publications (10 Years): 30

Top Venues

Publications

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) (2023)
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) (2023)
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) (2022)
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) (2021)
Marmar Moussa, Ion I. Mandoiu
SC1: A Tool for Interactive Web-Based Single-Cell RNA-Seq Data Analysis. J. Comput. Biol. 28 (8) (2021)
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) (2021)
Samuel Sledzieski, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal
TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference. PSB (2021)
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) (2021)
Marmar Moussa, Ion I. Mandoiu
Computational Cell Cycle Analysis of Single Cell RNA-Seq Data. ICCABS (2020)
Elham Sherafat, Jordan Force, Ion I. Mandoiu
Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy. BMC Bioinform. (18) (2020)
Marmar Moussa, Ion I. Mandoiu
SC1: A Tool for Interactive Web-Based Single Cell RNA-Seq Data Analysis. ISBRA (2020)
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)
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)
Fahad Alqahtani, Ion I. Mandoiu
Statistical Mitogenome Assembly with RepeaTs. J. Comput. Biol. 27 (9) (2020)
Fahad Alqahtani, Ion I. Mandoiu
Mitochondrial Haplogroup Assignment for High-Throughput Sequencing Data from Single Individual and Mixed DNA Samples. ISBRA (2020)
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) (2019)
Fahad Alqahtani, Ion I. Mandoiu
SMART2: Multi-library Statistical Mitogenome Assembly with Repeats. ICCABS (2019)
Marmar Moussa, Ion I. Mandoiu
Locality Sensitive Imputation for Single Cell RNA-Seq Data. J. Comput. Biol. 26 (8) (2019)
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 (2019)
Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
Workshop on Computational Advances in Molecular Epidemiology. BCB (2019)
Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
ACM-BCB 2018 Computational Advances in Molecular Epidemiology (CAME) Chairs' Welcome. BCB (2018)
Marmar Moussa, Ion I. Mandoiu
SC1: A web-based single cell RNA-seq analysis pipeline. ICCABS (2018)
Marmar Moussa, Ion I. Mandoiu
Locality Sensitive Imputation for Single-Cell RNA-Seq Data. ISBRA (2018)
Fahad Alqahtani, Ion I. Mandoiu
Statistical Mitogenome Assembly with Repeats. ICCABS (2018)
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) (2017)
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) (2017)
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) (2017)
Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
CAME 2017: 6th Workshop on Computational Advances in Molecular Epidemiology. BCB (2017)
Igor Mandric, Sergey Knyazev, Cory Padilla, Frank Stewart, Ion I. Mandoiu, Alex Zelikovsky
Metabolic Analysis of Metatranscriptomic Data from Planktonic Communities. ISBRA (2017)
Tyler Daddio, Ion I. Mandoiu
Pairing T Cell Receptor α and β sequences using pooling and min-cost flows. ICCABS (2016)
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) (2015)
Ekaterina Nenastyeva, Alex Zelikovsky, Yurij Ionov, Ion I. Mandoiu
Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire. ICCABS (2015)
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) (2015)
Adrian Caciula, Olga Glebova, Alexander Artyomenko, Serghei Mangul, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky
Deterministic regression algorithm for transcriptome frequency estimation. ICCABS (2014)
James Lindsay, Hamed Salooti, Ion I. Mandoiu, Alexander Zelikovsky
ILP-based maximum likelihood genome scaffolding. BMC Bioinform. 15 (S-9) (2014)
Igor Mandric, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky
SILP3: Maximum likelihood approach to scaffolding. ICCABS (2014)
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) (2014)
Alexander Artyomenko, Nicholas Mancuso, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu
kGEM: An EM-based algorithm for local reconstruction of viral quasispecies. ICCABS (2013)
James Lindsay, Craig E. Nelson, Ion I. Mandoiu
Towards whole transcriptome deconvolution using single-cell data. ICCABS (2013)
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) (2013)
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) (2013)
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) (2013)
Nicholas Mancuso, Alexander Artyomenko, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu
Estimation of viral population structure from amplicon-based reads. ICCABS (2013)
Gabriel Ilie, Alex Zelikovsky, Ion I. Mandoiu
Reference assisted nucleic acid sequence reconstruction from mass spectrometry data. ICCABS (2013)
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)
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)
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) (2013)
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)
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)
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) (2012)
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)
Sahar Al Seesi, Ion I. Mandoiu
Workshop: Inference of allele specific expression levels from RNA-Seq data. ICCABS (2012)
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)
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)
Jianer Chen, Ion I. Mandoiu, Raj Sunderraman, Jianxin Wang, Alexander Zelikovsky
Guest Editors' Introduction. BMC Bioinform. 13 (S-10) (2012)
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)
James Lindsay, Hamed Salooti, Alexander Zelikovsky, Ion I. Mandoiu
Scalable genome scaffolding using integer linear programming. BCB (2012)
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) (2012)
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) (2012)
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)
Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky
Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms Mol. Biol. 6 (2011)
Bogdan Pasaniuc, Robert S. Garfinkel, Ion I. Mandoiu, Alexander Zelikovsky
Optimal Testing of Digital Microfluidic Biochips. INFORMS J. Comput. 23 (4) (2011)
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) (2011)
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)
Marius Nicolae, Ion I. Mandoiu
Accurate Estimation of Gene Expression Levels from DGE Sequencing Data. ISBRA (2011)
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) (2011)
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)
Marius Nicolae, Ion I. Mandoiu
Poster: Empirical comparison of protocols for sequencing-based gene and isoform expression profiling. ICCABS (2011)
Jorge Duitama, Pramod Kumar Srivastava, Ion I. Mandoiu
Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data. ICCABS (2011)
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)
Nicholas Mancuso, Bassam Tork, Pavel Skums, Ion I. Mandoiu, Alexander Zelikovsky
Viral quasispecies reconstruction from amplicon 454 pyrosequencing reads. BIBM Workshops (2011)
Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alexander Zelikovsky
Poster: ViSpA: Viral spectrum assembling method. ICCABS (2011)
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)
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) (2010)
Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alexander Zelikovsky
Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data. WABI (2010)
Justin Kennedy, Ion I. Mandoiu, Bogdan Pasaniuc
GEDI: Scalable Algorithms for Genotype Error Detection and Imputation CoRR (2009)
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) (2009)
Ion I. Mandoiu
Genotype and Haplotype Reconstruction from Low-Coverage Short Sequencing Reads. BICoB (2009)
Bogdan Pasaniuc, Justin Kennedy, Ion I. Mandoiu
Imputation-Based Local Ancestry Inference in Admixed Populations. ISBRA (2009)
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) (2009)
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) (2008)
Bhaskar DasGupta, Jin Jun, Ion I. Mandoiu
Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP. APBC (2008)
Justin Kennedy, Ion I. Mandoiu, Bogdan Pasaniuc
Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity. J. Comput. Biol. 15 (9) (2008)
Alexander Gusev, Ion I. Mandoiu, Bogdan Pasaniuc
Highly Scalable Genotype Phasing by Entropy Minimization. IEEE ACM Trans. Comput. Biol. Bioinform. 5 (2) (2008)
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)
Sudha Balla, Sanguthevar Rajasekaran, Ion I. Mandoiu
Faster greedy algorithms for Multiple Degenerate Primer Selection. BIBE (2008)
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) (2007)
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) (2007)
Sudha Balla, Sanguthevar Rajasekaran, Ion I. Mandoiu
Efficient Algorithms for degenerate Primer Search. Int. J. Found. Comput. Sci. 18 (4) (2007)
Justin Kennedy, Ion I. Mandoiu, Bogdan Pasaniuc
Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity. WABI (2007)
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) (2007)
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) (2006)
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) (2006)
Ion I. Mandoiu, Claudia Prajescu
High-Throughput SNP Genotyping by SBE/SBH. International Conference on Computational Science (2) (2006)
Bogdan Pasaniuc, Ion I. Mandoiu
Highly Scalable Genotype Phasing by Entropy Minimization. EMBC (2006)
Ion I. Mandoiu, Dragos Trinca
Exact and Approximation Algorithms for DNA Tag Set Design. J. Comput. Biol. 13 (3) (2006)
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)
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) (2005)
Ion I. Mandoiu, Claudia Prajescu, Dragos Trinca
Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays. Trans. Comp. Sys. Biology 2 (2005)
Marek Karpinski, Ion I. Mandoiu, Alexander Olshevsky, Alexander Zelikovsky
Improved Approximation Algorithms for the Quality of Service Multicast Tree Problem. Algorithmica 42 (2) (2005)

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Publication Activity (10 Years)

Top Topics

Top Venues

Ion I. Mandoiu