| 2021 | PSB | TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network Inference. | Samuel Sledzieski, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal |
| 2011 | WABI | Maximum Likelihood Estimation of Incomplete Genomic Spectrum from HTS Data. | Serghei Mangul, Irina Astrovskaya, Marius Nicolae, Bassam Tork, Ion I. Mandoiu, Alexander Zelikovsky |
| 2010 | WABI | Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data. | Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alexander Zelikovsky |
| 2008 | APBC | Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP. | Bhaskar DasGupta, Jin Jun, Ion I. Mandoiu |
| 2008 | BIBE | Faster greedy algorithms for Multiple Degenerate Primer Selection. | Sudha Balla, Sanguthevar Rajasekaran, Ion I. Mandoiu |
| 2008 | RECOMB | Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events during Mammalian Evolution. | Jin Jun, Paul Ryvkin, Edward Hemphill, Ion I. Mandoiu, Craig E. Nelson |
| 2007 | WABI | Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity. | Justin Kennedy, Ion I. Mandoiu, Bogdan Pasaniuc |
| 2006 | ICCS | Minimum Multicolored Subgraph Problem in Multiplex PCR Primer Set Selection and Population Haplotyping. | Mohammad Taghi Hajiaghayi, Kamal Jain, Lap Chi Lau, Ion I. Mandoiu, Alexander Russell, Vijay V. Vazirani |
| 2006 | ICCS | High-Throughput SNP Genotyping by SBE/SBH. | Ion I. Mandoiu, Claudia Prajescu |
| 2005 | APBC | Improved algorithms for multiplex PCR primer set selection with amplification length constraints. | Kishori M. Konwar, Ion I. Mandoiu, Alexander Russell, Alexander A. Shvartsman |
| 2005 | CPM | Exact and Approximation Algorithms for DNA Tag Set Design. | Ion I. Mandoiu, Dragos Trinca |
| 2005 | ICCS | Highly Scalable Algorithms for Robust String Barcoding. | Bhaskar DasGupta, Kishori M. Konwar, Ion I. Mandoiu, Alexander A. Shvartsman |
| 2005 | ICCS | Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays. | Ion I. Mandoiu, Claudia Prajescu, Dragos Trinca |
| 2003 | ASPDAC | Highly scalable algorithms for rectilinear and octilinear Steiner trees. | Andrew B. Kahng, Ion I. Mandoiu, Alexander Zelikovsky |
| 2003 | GLOBECOM | Primal-dual algorithms for QoS multimedia multicast. | Gruia Calinescu, Cristina G. Fernandes, Ion I. Mandoiu, Alexander Olshevsky, K. Yang, Alexander Zelikovsky |
| 2003 | ICCAD | The Y-Architecture for On-Chip Interconnect: Analysis and Methodology. | Hongyu Chen, Chung-Kuan Cheng, Andrew B. Kahng, Ion I. Mandoiu, Qinke Wang, Bo Yao |
| 2003 | ICCAD | Layout-Aware Scan Chain Synthesis for Improved Path Delay Fault Coverage. | Puneet Gupta, Andrew B. Kahng, Ion I. Mandoiu, Puneet Sharma |
| 2003 | ICCAD | Evaluation of Placement Techniques for DNA Probe Array Layout. | Andrew B. Kahng, Ion I. Mandoiu, Sherief Reda, Xu Xu, Alexander Zelikovsky |
| 2003 | ICCD | Design Flow Enhancements for DNA Arrays. | Andrew B. Kahng, Ion I. Mandoiu, Sherief Reda, Xu Xu, Alexander Zelikovsky |
| 2003 | RECOMB | Engineering a scalable placement heuristic for DNA probe arrays. | Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky |
| 2003 | WCNC | Power efficient range assignment in ad-hoc wireless networks. | Ernst Althaus, Gruia Calinescu, Ion I. Mandoiu, Sushil K. Prasad, N. Tchervenski, Alexander Zelikovsky |
| 2003 | WADS | Improved Approximation Algorithms for the Quality of Service Steiner Tree Problem. | Marek Karpinski, Ion I. Mandoiu, Alexander Olshevsky, Alexander Zelikovsky |
| 2002 | ICCAD | Non-tree routing for reliability and yield improvement. | Andrew B. Kahng, Bao Liu, Ion I. Mandoiu |
| 2002 | VLSID | Floorplan Evaluation with Timing-Driven Global Wireplanning, Pin Assignment and Buffer/Wire Sizing. | Christoph Albrecht, Andrew B. Kahng, Ion I. Mandoiu, Alexander Zelikovsky |
| 2002 | WABI | Border Length Minimization in DNA Array Design. | Andrew B. Kahng, Ion I. Mandoiu, Pavel A. Pevzner, Sherief Reda, Alexander Zelikovsky |
| 2001 | ASPDAC | Provably good global buffering by multi-terminal multicommodity flow approximation. | Feodor F. Dragan, Andrew B. Kahng, Ion I. Mandoiu, Sudhakar Muddu, Alexander Zelikovsky |
| 2001 | ICCAD | Minimum-Buffered Routing of Non-Critical Nets for Slew Rate and Reliability Control. | Charles J. Alpert, Andrew B. Kahng, Bao Liu, Ion I. Mandoiu, Alexander Zelikovsky |
| 2001 | SODA | Practical approximation algorithms for zero- and bounded-skew trees. | Alexander Zelikovsky, Ion I. Mandoiu |
| 2001 | WADS | Practical Approximation Algorithms for Separable Packing Linear Programs. | Feodor F. Dragan, Andrew B. Kahng, Ion I. Mandoiu, Sudhakar Muddu, Alexander Zelikovsky |
| 2000 | ICCAD | Provably Good Global Buffering Using an Available Buffer Block Plan. | Feodor F. Dragan, Andrew B. Kahng, Ion I. Mandoiu, Sudhakar Muddu, Alexander Zelikovsky |
| 1999 | ICCAD | A new heuristic for rectilinear Steiner trees. | Ion I. Mandoiu, Vijay V. Vazirani, Joseph L. Ganley |
| 1999 | SODA | A Primal-Dual Schema Based Approximation Algorithm for the Element Connectivity Problem. | Kamal Jain, Ion I. Mandoiu, Vijay V. Vazirani, David P. Williamson |